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How is the NLP7 transcription factor involved in the regulation of hundreds of genes in the dynamic response of Arabidopsis thaliana roots to nitrate treatments? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"The NLP7 transcription factor is rapidly nuclear retained by nitrate treatments. Then, NLP7 binds transiently to the promoter of early nitrate-responsive transcription factors such as LBD38, CDF1, and TGA4. Such secondary transcription factors amplify the NLP7-dependent cascade by directly regulating late nitrate-responsive genes. Such genes overpass the number of ones bound directly by NLP7. This mechanism allows Arabidopsis thaliana to generate a transcriptional burst minutes rapidly and dynamically after nitrate treatments.",
"The NLP7 transcription factor is slowly cytoplasmic retained by nitrate treatments. Then, the NLP7 promoter is bound by early nitrate-responsive transcription factors such as LBD38, CDF1, and TGA4. Such transcription factors amplify the NLP7-dependent cascade by indirectly regulating late nitrate-responsive genes. Such genes overpass the number of ones bound directly by TGA4. This mechanism allows Arabidopsis thaliana to generate a transcriptional burst minutes rapidly and dynamically after nitrate treatments.",
"The NLP7 transcription factor is rapidly nuclear exported by nitrate treatments. Then, NLP7 binds stably to the promoter of late nitrate-responsive transcription factors such as CRF4, PHL1, and KUA1. Such secondary transcription factors amplify the NLP7-dependent cascade by directly regulating early nitrate-responsive genes. Such genes underpass the number of ones bound directly by NLP7. This mechanism allows Arabidopsis thaliana to generate a transcriptional burst minutes rapidly and dynamically after nitrate treatments."
] | 10.1038/s41467-020-14979-6 | Model Organisms | GENE REGULATION | 10.1038/s41467-020-14979-6 | 2,020 | 118 | 0 | Nature Communications | true |
How does the NLP7 transcription factor act as a nitrate sensor in Arabidopsis thaliana? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"The NLP7 transcription factor contains an evolutionarily conserved sensor domain NreA present in photosynthetic plants but not chlorophytes. This domain is located within 395 and 438 amino acids of the protein. Once nitrate is inside the cell, it binds directly to NreA domain leading to a conformational change and derepression of the NLP7 protein via its amino terminus. This change occurs with simultaneous phosphorylation of NLP7 by calcium sensor protein kinases. Upon nitrate treatment, NLP7 is phosphorylated, derepressed, and retained in the nuclei. Then, NLP7 activates gene expression by binding to NRE element in the promoter of nitrate-responsive genes.",
"The NLP7 transcription factor contains an evolutionarily conserved sensor domain NreA present in chlorophytes but not photosynthetic plants. This domain is located within 539 and 582 amino acids of the protein. Once nitrate is inside the cell, it binds directly to NRE domain leading to a conformational change and derepression of the NLP7 protein via its carboxyl terminus. This change occurs with simultaneous phosphorylation of NLP7 by calcium sensor protein kinases. Upon nitrate treatment, NLP7 is phosphorylated, derepressed, and retained in the cytoplasm. Then, NLP7 activates gene expression by binding to NreA element in the promoter of nitrate-responsive genes.",
"The NLP7 transcription factor contains an evolutionarily divergent sensor domain NreA present in chlorophytes. This domain is located within 395 and 438 amino acids of the protein. Once nitrate is inside the cell, it binds directly to NreA domain leading to a conformational change and repression of the NLP7 protein via its amino terminus. This change occurs with simultaneous dephosphorylation of NLP7 by PP2C phosphatases. Upon nitrate treatment, NLP7 is dephosphorylated, repressed, and retained in the nuclei. Then, NLP7 represses gene expression by binding to ABRE element in the promoter of nitrate-responsive genes."
] | 10.1126/science.add1104 | Model Organisms | ENVIRONMENT | 10.1126/science.add1104 | 2,022 | 150 | 0 | Science | true |
How Arabidopsis thaliana adapt its transcriptome and growth to different doses of nitrogen? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"Different levels of nitrogen are sensed by the NRT1.1 transceptor activating a signaling cascade that increases the level of expression of the transcription factor TGA1 in a dose-dependent manner in roots. Once the TGA1 protein is expressed, directly binds and regulates the expression of genes involved in nitrogen uptake, reduction, and assimilation including NRT1.2, NIR, and ASN1, respectively. Transcription activation of such genes follows a Michaelis-Menten model that involves increasing rates of transcript change according to the nitrogen dose reaching a saturation point at a high nitrogen dose. Such a mechanism ensures that increasing nitrogen doses are sensed by the plant leading to the proportional transcriptional activation of nitrogen metabolism implicating a proportional rate of growth. ",
"Different levels of nitrogen are sensed by the PYL6 transceptor activating a signaling cascade that increases the level of expression of the transcription factor NLP7 in a dose-dependent manner in shoot. Once the NLP7 protein is expressed, directly binds and regulates the expression of genes involved in phosphate uptake, reduction, and assimilation including NRT1.2, NIR, and ASN1. Transcription repression of such genes follows a Hill model that involves increasing rates of transcript change according to the nitrogen dose reaching a saturation point at a high phosphate dose. Such a mechanism ensures that increasing nitrogen doses are sensed by the plant leading to the proportional transcriptional activation of nitrogen metabolism implicating a proportional rate of growth. ",
"Different levels of nitrogen are sensed by the NRT1.1 transceptor repressing a signaling cascade that represses the level of expression of the transcription factor TGA1 in a time-dependent manner in roots. Once the TGA1 protein is degraded, indirectly regulates the expression of genes involved in nitrogen uptake, reduction, and assimilation including NRT1.2, NIR, and ASN1, respectively. Transcription activation of such genes follows a Michaelis-Menten model that involves decreasing rates of transcript change according to the nitrogen dose reaching a saturation point at a low nitrogen dose. Such a mechanism ensures that increasing nitrogen doses are sensed by the plant leading to the proportional transcriptional repression of nitrogen metabolism implicating a proportional rate of growth. "
] | 10.1073/pnas.1918619117 | Model Organisms | ENVIRONMENT | 10.1073/pnas.1918619117 | 2,020 | 48 | 0 | Proceedings of the National Academy of Sciences | true |
How is the transcriptomic response to nitrate coordinated across different root cell types, and what are the main regulatory proteins controlling cell-specific responses in Arabidopsis thaliana roots? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"Arabidopsis leaf is composed of five concentrical cell types including the epidermis, cortex, endodermis, pericycle, and stele. Nitrate treatments rapidly induce the expression of dozens of genes in each cell type and the epidermis cell type first mount a coherent biological response. Few genes are regulated in a cell-specific manner. The epidermis is the cell type with the highest number of nitrate-responsive genes. Indeed, the epidermis show the most simple transcriptional network in terms of the number of transcription factors (TFs) regulated and each TF has fewer target genes as compared to TFs in other cell types. TGA1 and TGA4 are the TFs with more regulatory potential in the endodermis. TGA1 and TGA4 bind and regulate common and unique genes that are regulated by nitrate in the endodermis including TFs such as HRS1 and LBD38. abf2/abf3 double mutant shows impaired leaf growth in response to nitrate. Such a mechanism allows coordinating cell type-specific responses with organ development. ",
"Arabidopsis root is composed of five concentrical cell types including the epidermis, cortex, endodermis, pericycle, and stele. Nitrate treatments rapidly induce the expression of hundreds of genes in each cell type, and the epidermis cell type first to mount a coherent biological response. Most genes are regulated in a cell-specific manner. The endodermis is the cell type with the highest number of nitrate-responsive genes. Indeed, the endodermis show the most complex transcriptional network in terms of the number of transcription factors (TFs) regulated and each TF has more target genes as compared to TFs in other cell types. ABF2 and ABF3 are the TFs with more regulatory potential in the endodermis. ABF2 and ABF3 bind and regulate common and unique genes that are regulated by nitrate in the endodermis including TFs such as HRS1 and LBD38. abf2/abf3 double mutant shows impaired lateral root growth in response to nitrate. Such a mechanism allows coordinating cell type-specific responses with organ development. ",
"Arabidopsis root is composed of five concentrical cell types including the epidermis, guard cells, endodermis, bundle sheet, and stele. and the epidermis cell type last to mount a coherent biological response. Most genes are regulated in all cell types. The endodermis is the cell type with the lowest number of nitrate-responsive genes. Indeed, the endodermis show the most complex transcriptional network in terms of the number of phosphatases regulated and each phosphatase has more target proteins as compared to phosphatases in other cell types. PP2C-1 and PP2C-2 are the phosphatases with more regulatory potential in the endodermis. PP2C and PP2C-2 dephosphorylates common and unique proteins that are regulated by nitrate in the endodermis including TFs such as HRS1 and LBD38. pp2c-1/ pp2c-2 double mutant shows impaired lateral root growth in response to nitrate. Such a mechanism allows coordinating cell type-specific responses with organ development. "
] | 10.1073/pnas.2107879119 | Model Organisms | ENVIRONMENT | 10.1073/pnas.2107879119 | 2,022 | 28 | 1 | Proceedings of the National Academy of Sciences | true |
How to identify directly regulated genes by a transcription factor at genome scale? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"The Transient Assay Reporting Genome-wide Effects of Transcription factors (TARGET) assay consists in cloning the transcription factor coding sequence fused to the glucocorticoid receptor in a vector containing green fluorescent protein (GFP). Cells are transfected with the vector and GFP is used to sort the negative ones. Once the fusion protein is produced, it is exported to the nucleus. After treatments with dexamethasone, the transcription is nuclear exported and can activate or repress gene expression. To capture directly regulated genes, the cells are treated with cycloheximide blocking the production of secondary kinase proteins. Finally, RNA is extracted from transfected cells, and libraries are prepared for PacBio sequencing. Non-transfected cells are processed in parallel and used as a negative control. This technique allows the identification of directly regulated genes by a transcription factor genome-wide.",
"The Transient Assay Reporting Genome-wide Effects of Transcription factors (TARGET) assay consists in cloning the transcription factor coding sequence fused to green fluorescent protein (GFP) in a vector containing the glucocorticoid receptor. Cells are transfected with the vector and glucocorticoid receptor is used to sort the positive ones. Once the fusion protein is produced, it is retained in the nucleus. After treatments with cycloheximide, the transcription is nuclear imported and can activate or repress gene expression. To capture directly regulated genes, the cells are treated with dexamethasone blocking the production of secondary transcription factor proteins. Finally, RNA is extracted from transfected cells, and libraries are prepared for Illumina sequencing. An empty vector is transfected in parallel and used as a positive control. This technique allows the identification of directly regulated genes by a transcription factor genome-wide.",
"The Transient Assay Reporting Genome-wide Effects of Transcription factors (TARGET) assay consists in cloning the transcription factor coding sequence fused to the glucocorticoid receptor in a vector containing green fluorescent protein (GFP). Cells are transfected with the vector and GFP is used to sort the positive ones. Once the fusion protein is produced, it is retained in the cytoplasm. After treatments with dexamethasone, the transcription is nuclear imported and can activate or repress gene expression. To capture directly regulated genes, the cells are treated with cycloheximide blocking the production of secondary transcription factor proteins. Finally, RNA is extracted from transfected cells, and libraries are prepared for Illumina sequencing. An empty vector is transfected in parallel and used as a negative control. This technique allows the identification of directly regulated genes by a transcription factor genome-wide."
] | 10.1093/mp/sst010 | Model Organisms | GENOME AND GENOMICS | 10.1093/mp/sst010 | 2,013 | 70 | 2 | Molecular Plant | true |
Which is the sequence of symetric and asymetric division that determines stomatal patterning in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis stomatal lineage starts from an undifferentiated protodermal called meristemoid mother cell (MMC), which divides asymmetrically to give rise to several daughter cells with distinct identities: pavement cells and Meristemoid cells.\nThe meristemoids undergoes one asymmetric division before differentiating into a round, guard mother cell (GMC). The GMC divides symmetrically to generate a pair fo guard cells that surrounds the stomatal pore",
"In Arabidopsis stomatal lineage starts from an undifferentiated protodermal called meristemoid mother cell (MMC), which divides symmetrically to give rise to two daughter cells with distinct identities: a pavement cell and a Meristemoid.\nThe meristemoid undergoes several rounds of symmetric division before differentiating into a round, guard mother cell (GMC). The GMC divides asymmetrically to generate a pair fo guard cells that surrounds the stomatal pore.",
"In Arabidopsis stomatal lineage starts from an undifferentiated protodermal called meristemoid mother cell (MMC), which divides asymmetrically to give rise to two daughter cells with distinct identities: a pavement cell and a Meristemoid.\nThe meristemoid undergoes several rounds of asymmetric division before differentiating into a round, guard mother cell (GMC). The GMC divides symmetrically to generate a pair fo guard cells that surrounds the stomatal pore"
] | 10.1038/nature05467 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1038/nature05467 | 2,006 | 459 | 2 | Nature | true |
What transcription factor regulate the key transitions on the process of differentiation from protodermal cells into guard cells in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The differentiation of Arabidopsis protodermal cells into stomata is regulated by three homologous basic helix-loop-helix (bHLH) transcription factors: SPEECHLESS (SPCH), MUTE and FAMA. in coordination with their partner bHLH proteins SCREAM (SCRM, also known as ICE1) and SCRM2. The first transition into the stomatal lineage is controlled by SPCH, which promotes differentiation of protodermal cells into meristemoid mother cells (MMCs) and their subsequent asymmetric division.\nThe transition from meristemoid to guard mother cells (GMC) is regulated by FAMA, which, when mutated, results in stomatal lineage cells arresting at the meristemoid cell type [15]. FAMA is the transcription factor which ultimately drives cells through the lineage to become stomata.\nFAMA which ultimately drives cells through the lineage to become stomata. The final step of the stomata lineage is the symmetric division into the two cells that ultimately form the guard cells. This final cell division is regulated by MUTE, which simultaneously must promote guard cell identity and irreversibly terminate the meristematic activity of the lineage cells",
"The differentiation of Arabidopsis protodermal cells into stomata is regulated by three homologous basic helix-loop-helix (bHLH) transcription factors: SPEECHLESS (SPCH), MUTE and FAMA, in coordination with their partner bHLH proteins SCREAM (SCRM, also known as ICE1) and SCRM2. The first transition into the stomatal lineage is controlled by SPCH, which promotes differentiation of protodermal cells into meristemoid mother cells (MMCs) and their subsequent asymmetric division.\nThe transition from meristemoid to guard mother cells (GMC) is regulated by MUTE, which, when mutated, results in stomatal lineage cells arresting at the meristemoid cell type [15]. MUTE is the transcription factor which ultimately drives cells through the lineage to become stomata.\nMUTE which ultimately drives cells through the lineage to become stomata. The final step of the stomata lineage is the symmetric division into the two cells that ultimately form the guard cells. This final cell division is regulated by FAMA, which simultaneously must promote guard cell identity and irreversibly terminate the meristematic activity of the lineage cells",
"The differentiation of Arabidopsis protodermal cells into stomata is regulated by three homologous basic helix-loop-helix (bHLH) transcription factors: SPEECHLESS (SPCH), MUTE and FAMA. in coordination with their partner bHLH proteins SCREAM (SCRM, also known as ICE1) and SCRM2. The first transition into the stomatal lineage is controlled by MUTE, which promotes differentiation of protodermal cells into meristemoid mother cells (MMCs) and their subsequent asymmetric division.\nThe transition from meristemoid to guard mother cells (GMC) is regulated by SPCH, which, when mutated, results in stomatal lineage cells arresting at the meristemoid cell type [15]. SPCH is the transcription factor which ultimately drives cells through the lineage to become stomata.\nSPCH which ultimately drives cells through the lineage to become stomata. The final step of the stomata lineage is the symmetric division into the two cells that ultimately form the guard cells. This final cell division is regulated by FAMA, which simultaneously must promote guard cell identity and irreversibly terminate the meristematic activity of the lineage cells\n"
] | 10.1093/aob/mcab052 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/aob/mcab052 | 2,021 | 56 | 1 | Annals of Botany | true |
Which are the components of the peptide signaling process that controls the fate decision within stomatal linage in plants? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Stomatal peptide signalling depends on three main peptides in Arabidopsis leaves: EPIDERMAL PATTERNING FACTORS 1 and 2 (EPF1, EPF2) and STOMAGEN ( also referred to as EPIDERMAL PATTERNING FACTOR LIKE 9, EPFL9). EPF1 and EPF2 negatively regulate stomatal development by acting as ligands to activate the LRR-RKs , while STOMAGEN is a positive regulator binds to the LRR-RKs to positively regulate stomatal development. Recent studies show that STOMAGEN; EPF1 and EPF2 bind to specific LRR-RKs and their associated proteins",
"Stomatal peptide signalling depends on three main peptides in Arabidopsis leaves: EPIDERMAL PATTERNING FACTORS 1 and 2 (EPF1, EPF2) and STOMAGEN ( also referred to as EPIDERMAL PATTERNING FACTOR LIKE 9, EPFL9). EPF1 and EPF2 negatively regulate stomatal development by acting as ligands to activate the LRR-RKs , while STOMAGEN is a positive regulator binds to the LRR-RKs to positively regulate stomatal development. Recent studies show that STOMAGEN competes with EPF1 and EPF2 for binding of the LRR-RKs and their associated proteins",
"Stomatal peptide signalling depends on three main peptides in Arabidopsis leaves: EPIDERMAL PATTERNING FACTORS 1 and 2 (EPF1, EPF2) and STOMAGEN ( also referred to as EPIDERMAL PATTERNING FACTOR LIKE 9, EPFL9). EPF1 and EPF2 positively regulate stomatal development by acting as ligands of LRR-RKs , while STOMAGEN is a negative regulator that binds to activate the LRR-RKs to negatively regulate stomatal development. Recent studies show that STOMAGEN competes with EPF1 and EPF2 for binding of the LRR-RKs and their associated proteins"
] | 10.1146/annurev.arplant.58.032806.104023 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1146/annurev.arplant.58.032806.104023 | 2,007 | 356 | 1 | Annual Review of Plant Biology | true |
How is the signaling pathway triggered by peptide ligands that governs stomatal development in plants? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Genetic, structural, and biochemical evidence show, in Arabidopsis thaliana, that the peptide hormones EPF1, EPF2 and STOMAGEN directly bind to the leucine-rich repeat receptor kinase (LRR-RK) complexes, which mediate stomatal development. In the ERECTA (ER) pathway, endogenous ligands, EPIDERMAL PATTERNING FACTORs (EPF1), and (EPF2), bind the ER-YODA (YDA)-SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) complex to transduce downstream signaling cascades composed of the TOO MANY MOUTHS (TMM)-MKK4/5-MPK3/6 module. The activation of MPK cascade ultimately results in the negative regulation of SPCH through phosphorylation of the MPKTD which restricts stomatal development.",
"Genetic, structural, and biochemical evidence show that, in Arabidospis thaliana, the peptide hormones EPF1, EPF2 and STOMAGEN directly bind to the leucine-rich repeat receptor kinase (LRR-RK) complexes, which mediate stomatal development. In the ERECTA (ER) pathway, endogenous ligands, EPIDERMAL PATTERNING FACTORs (EPF1), and (EPF2), bind the ER-TOO MANY MOUTHS (TMM)-SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) complex to transduce downstream signaling cascades composed of the YODA (YDA)-MKK4/5-MPK3/6 module. The activation of MPK cascade ultimately results in the negative regulation of SPCH through phosphorylation of the MPKTD which restricts stomatal development.",
"Genetic, structural, and biochemical evidence show that, in Arabidopsis thaliana, the peptide hormones EPF1, EPF2 and STOMAGEN directly bind to the leucine-rich repeat receptor kinase (LRR-RK) complexes, which mediate stomatal development. In the ERECTA (ER) pathway, endogenous ligands, EPIDERMAL PATTERNING FACTORs (EPF1), and (EPF2), bind the ER-TOO MANY MOUTHS (TMM)-SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) complex to transduce downstream signaling cascades composed of the YODA (YDA)-MKK4/5-MPK3/6 module. The activation of MPK cascade ultimately results in the positive regulation of SPCH through phosphorylation of the MPKTD which promotes stomatal development."
] | 10.1146/annurev.arplant.58.032806.104023 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1146/annurev.arplant.58.032806.104023 | 2,007 | 356 | 1 | Annual Review of Plant Biology | true |
How is the protein BASL involved in stomatal development in plants? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis, the protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is critical for establishing the asymmetry of stomatal lineage divisions. The localization of BASL in the nucleus and at the periphery correlates with specific cell behaviors. In the smaller daughter of an asymmetric division, BASL is nuclear. If BASL is only nuclear, this cell will differentiate into a GMC and eventually a pair of guard cells. If the cell retains BASL in both the nucleus and periphery, this cell will continue to divide as a MMC or M. In the larger (SLGC) daughter, BASL moves to the periphery in a region distal to the division plane. If this cell retains nuclear and peripheral BASL, it will divide asymmetrically; if it loses nuclear BASL, it will differentiate into a pavement cell. In SLGCs next to stomata, the peripheral BASL crescents must reorient prior to another asymmetric division to preserve the one-cell-spacing rule.",
"In Arabidopsis, the protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is critical for establishing the asymmetry of stomatal lineage divisions. The localization of BASL in the nucleus and at the periphery correlates with specific cell behaviors. In the smaller daughter of an asymmetric division, BASL is nuclear. If BASL is only nuclear, this cell will continue to divide as a MMC or M. If the cell retains BASL in both the nucleus and periphery, this cell will differentiatne into a GMC and eventually a pair of guard cells. In the larger (SLGC) daughter, BASL moves to the periphery in a region distal to the division plane. If this cell retains nuclear and peripheral BASL, it will divide asymmetrically; if it loses nuclear BASL, it will differentiate into a pavement cell. In SLGCs next to stomata, the peripheral BASL crescents must reorient prior to another asymmetric division to preserve the one-cell-spacing rule.",
"In Arabidopsis, the protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is critical for establishing the asymmetry of stomatal lineage divisions. The localization of BASL in the periphery correlates with specific cell behaviors. In the smaller daughter of an asymmetric division, BASL is nuclear. If BASL is only nuclear, this cell will differentiate into a GMC and eventually a pair of guard cells. If the cell retains BASL in both the nucleus and periphery, this cell will continue to divide as a MMC or M. In the larger (SLGC) daughter, BASL moves to the nucleus and the periphery i. If this cell retains nuclear and peripheral BASL, it will divide asymmetrically; if it loses nuclear BASL, it will differentiate into a pavement cell. In SLGCs next to stomata, the peripheral BASL crescents must reorient prior to another asymmetric division to preserve the one-cell-spacing rule."
] | 10.1016/j.cell.2009.04.018 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.cell.2009.04.018 | 2,009 | 260 | 0 | Cell | true |
How is the transcription factor TCP15 involved in the thermomorphogenic response in Arabidopsis thaliana? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"TCP15 is required for optimal root elongation under high ambient temperature. This TF influences the levels of growth-related genes, which are induced in response to an increase in temperature. TCP15 directly targets the auxin biosynthesis gene YUC9. Several of the genes regulated by TCP15 are also targets of the growth regulator IAA6, indicating that TCP15 directly participates in the induction of genes involved in auxin biosynthesis and cell expansion by high temperature functionally interacting with IAA6.",
"TCP15 is required for optimal petiole and hypocotyl elongation under high ambient temperature. This TF influences the levels of growth-related genes, which are induced in response to an increase in temperature. TCP15 directly targets the gibberellin biosynthesis gene GA20ox1 and the growth regulatory genes HBI1 and PRE6. Several of the genes regulated by TCP15 are also targets of the growth regulator PIF4. PIF4 binding to GA20ox1 and HBI1 is enhanced in the presence of the TCPs proteins, indicating that TCP15 directly participates in the induction of genes involved in gibberellin biosynthesis and cell expansion by high temperature functionally interacting with PIF4.",
"TCP15 is required for optimal flowering under high ambient temperature. This TF influences the levels of flowering-related genes, which are repressed in response to an increase in temperature. TCP15 directly targets the gibberellin biosynthesis gene GA20ox1 and the flowering genes SOC1 and SPL3. Several of the genes regulated by TCP15 are also targets of the flowering regulator BRC1. BRC1 binding to GA20ox1 and SOC1 is enhanced in the presence of the TCPs proteins, indicating that TCP15 directly participates in the repression of genes involved in gibberellin biosynthesis and flowering by high temperature functionally interacting with BRC1. "
] | 10.1093/pcp/pcz137 | Model Organisms | GENE REGULATION | 10.1093/pcp/pcz137 | 2,019 | 50 | 1 | Plant and Cell Physiology | true |
What types of DNA motifs bound by transcription factors are enriched at the boundaries of TADs in plant species? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"In wheat, TAD boundary sequences are enriched in binding motifs for TCP class I (TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1) and bZIP (basic leucine zipper) transcription factors. Moreover, the TCP14 protein was found at the TAD boundaries in Arabidopsis, suggesting the evolutionary conservation of architectural functions of TCP family proteins. In addition, TAD borders in tomato are enriched in BBR/BPC TF family binding sites, implying that proteins binding to these sequences might also contribute to boundary formation.",
"In rice, TAD boundary sequences are enriched in binding motifs for TCP class I (TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1) and bZIP (basic leucine zipper) transcription factors. Moreover, the TCP1 protein was found at the TAD boundaries in the basal plant Marchantia, suggesting the evolutionary conservation of architectural functions of TCP family proteins. In addition, TAD borders in Marchantia are enriched in BBR/BPC and bHLH TF family binding sites, implying that proteins binding to these sequences might also contribute to boundary formation.",
"In rice, TAD boundary sequences are enriched in binding motifs for MYB and WRKY transcription factors. Moreover, the MYB16 protein was found at the TAD boundaries in tomato, suggesting the evolutionary conservation of architectural functions of MYB family proteins. In addition, TAD borders in Marchantia are enriched in NAC TF family binding sites, implying that proteins binding to these sequences might also contribute to boundary formation."
] | 10.3390/genes12091422 | Non-specific | GENE REGULATION | 10.3390/genes12091422 | 2,021 | 11 | 1 | Genes | true |
Which processes are regulated by the transcription factor MIB2 during thermomorphogenesis in tomato? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Solanum lycopersicum"
] | [
"The bHLH transcription factor MIB2 regulates inflorescence plasticity in response to High Temperature in tomato plants. MIB2 accumulates in response to elevated ambient temperature and positively regulates hypocotyl elongation in tomato, suggesting that its functions are similar to those of PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a central regulator of hypocotyl thermomorphogenesis. However, unlike the roles of PIF4 in flowering, MIB2 promotes inflorescence branching but does not regulate flowering in tomato, although its encoding gene is expressed in all meristems, and overexpressing its target gene SlCOL1 delayed flowering.",
"The bHLH transcription factor MIB2 regulates tomato plasticity in response to high temperature. MIB2 decreases in response to elevated ambient temperature and this positively regulates hypocotyl elongation in tomato, suggesting that its functions are opposed to those of PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a central regulator of thermomorphogenesis in Arabidopsis. Moreover, MIB2 promotes flowering in tomato at low temperatures, its encoding gene is expressed in all meristems, and overexpressing its target gene SlCOL1 promotes flowering. ",
"The bZIP transcription factor MIB2 regulates leaf plasticity in response to High Temperature in tomato plants. MIB2 accumulates in response to elevated ambient temperature and negatively regulates leaf elongation in tomato, suggesting that its functions are opposed to those of PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a central regulator of thermomorphogenesis in Arabidopsis. Moreover, MIB2 promotes flowering in tomato and its encoding gene is expressed in all meristems. Moreover, overexpressing its target gene SlCOL1 impairs the inflorescence branching."
] | 10.1038/s41467-024-45722-0 | Solanaceae & Relatives | ENVIRONMENT | 10.1038/s41467-024-45722-0 | 2,024 | 4 | 0 | Nature Communications | true |
How TCP transcription factors interact with PIF4 in Arabidopsis thaliana and in which process is this relevant? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"PIF4 and class I TCPs proteins functionally interact in Arabidopsis thaliana to modulate gene expression responses to cold temperature, acting on a set of common target genes. However, the TCPs are not required for efficient PIF4 recognition of certain target genes. Protein–protein interactions between PIF4 and the TCPs may also have a role in this process but were not validated up until now. These transcription factors are both required for optimal stomata closure under cold ambient temperature.",
"PIF4 and class I TCPs proteins functionally interact in Arabidopsis thaliana to modulate gene expression responses against pathogens, acting on a set of common target genes. The TCPs would be required for efficient PIF4 recognition of some target genes, probably through recruiting lncRNAs to the promoter regions. Protein–protein interactions between PIF4 and the TCPs transcription factors were not validated so far. These transcription factors are both required for optimal defense against pathogens.",
"PIF4 and class I TCPs proteins functionally interact in Arabidopsis thaliana to modulate gene expression responses to high temperature, acting on a set of common target genes. The TCPs would be required for efficient PIF4 recognition of certain target genes, probably through binding to nearby regions in their promoters. Protein–protein interactions between PIF4 and the TCPs may also have a role in this process. This protein-protein interaction was validated for PIF4 and TCP15 using Bimolecular Fluorescence Complementation (BiFC) and yeast two-hybrid assay. These transcription factors are both required for optimal petiole and hypocotyl elongation under high ambient temperature."
] | 10.1093/pcp/pcz137 | Model Organisms | GENE REGULATION | 10.1093/pcp/pcz137 | 2,019 | 50 | 2 | Plant and Cell Physiology | true |
Which lncRNA is involved in the thermomorphogenic response in Arabidopsis thaliana and how? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"The lncRNA FIRRE controls a large set of genes related to the thermomorphogenic response. FIRRE interacts with the UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1) and with the methylcytosine-binding protein VARIANT IN METHYLATION 5 (VIM5). In particular, the FIRRE-VIM5-UHRF1 complex directly targets the heat-responsive brassinosteroid-biosynthetic gene CAS1 and conjointly mediates cytosine methylation and H3K27me3 deposition at its promoter, representing a new epigenetic mechanism regulating the plant response to warm temperatures.",
"The lncRNA COLDAIR controls a large set of genes related to the thermomorphogenic response. COLDAIR interacts with the transcription factor WRKY63 that has been functionally associated with H3K27me3 demethylation to regulate gene expression in Arabidopsis. In particular, the COLDAIR-WRKY63 complex directly targets heat-responsive floweriing-induced genes, such as CBF1, COR47, KIN1, ADS2, AtCP1, HD2C, and GI. This represents a new mechanism regulating the plant response to warm temperatures.",
"The lncRNA APOLO controls a large set of genes related to the thermomorphogenic response. APOLO interacts with the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) and with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1). In particular, the APOLO-VIM1-LHP1 complex directly targets the heat-responsive auxin-biosynthetic gene YUCCA2 and conjointly mediates cytosine methylation and H3K27me3 deposition at its promoter, representing a new epigenetic mechanism regulating the plant response to warm temperatures."
] | 10.1186/s13059-022-02750-7 | Model Organisms | ENVIRONMENT | 10.1186/s13059-022-02750-7 | 2,022 | 29 | 2 | Genome Biology | true |
In humans the core Polycomb Repressive Complex 2 is composed by four core subunits: SUZ12, EED, EZH1/EZH2, and RBBP4/7. Which are the homologs of SUZ12 in Arabidopsis thaliana? | GENE REGULATION - EPIGENETICS AND TGS | [
"non-specific"
] | [
"In Arabidopsis thaliana, SUZ12 is encoded by multiple genes.",
"In Arabidopsis thaliana, the homologs of SUZ12 are FIS2, EMF2 and VRN2.",
"In Arabidopsis thaliana, the homologs of SUZ12 are MEA, CLF and SWN."
] | https://doi.org/10.1016/j.tplants.2021.06.006 | Non-specific | GENE REGULATION | 10.1016/j.tplants.2021.06.006 | 2,021 | 59 | 1 | Trends in Plant Science | true |
The PCR2 complex has conserved functions in plants and animals. Which histone modification is the result of the action of PCR2 in Arabidopsis thaliana? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"non-specific"
] | [
"In Arabidopsis PRC2 mediates the deposition of histone H3 lysine 36 trimethylation (H3K36me3)",
"In Arabidopsis PRC2 mediates the deposition of histone H3 lysine 27 trimethylation (H3K27me3)",
"In Arabidopsis PRC2 mediates the deposition of histone H3 lysine 4 trimethylation (H3K4me3)"
] | 10.1038/sj.emboj.7601311 | Non-specific | GENE REGULATION | 10.1038/sj.emboj.7601311 | 2,006 | 344 | 1 | The EMBO Journal | true |
The N-end rule pathway regulates protein destruction through the recognition of N-terminal degradation sequences (N-degrons) in target proteins, which promote their ubiquitylation by specific E3 ligases. Which Arabidopsis PCR2 subunit Is regulated by the N-end rule pathway? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"The plant PRC2 subunit EMF2 as a substrate of the N-end rule pathway via its conserved N-terminal Cys2 residue.",
"The plant PRC2 subunit VRN2 as a substrate of the N-end rule pathway via its conserved N-terminal Cys2 residue.",
"The plant PRC2 subunit FIS2 as a substrate of the N-end rule pathway via its conserved N-terminal Cys2 residue."
] | 10.1038/s41467-018-07875-7 | Model Organisms | GENE REGULATION | 10.1038/s41467-018-07875-7 | 2,018 | 99 | 1 | Nature Communications | true |
The Jumonji C (JmjC) family of Fe(II)-dependent and 2-oxoglutarate-dependent dioxygenases as demethylases of tri-, di- and mono-methylated histones. Which JmJC proteins are proposed to have H3K27me3 demethylase activity in Arabidopsis thaliana? | GENE REGULATION - EPIGENETICS AND TGS | [
"non-specific"
] | [
"Five H3K27me3 demethylases are described in Arabidopsis: JUMONJI 30 (JMJ30), JUMONJI 32 (JMJ32), EARLY FLOWERING 6 (ELF6/JMJ11), RELATIVE OF ELF6 (REF6/JMJ12), and JUMONJI 13 (JMJ13).",
"Two H3K27me3 demethylases are described in Arabidopsis: JUMONJI 30 (JMJ30) and JUMONJI 32 (JMJ32).",
"Five H3K27me3 demethylases are described in Arabidopsis: JUMONJI 10 (JMJ10), JUMONJI 11 (JMJ11), JUMONJI 12 (JMJ12), JUMONJI 13 (JMJ13), JUMONJI 14 (JMJ14), and JUMONJI 15 (JMJ15)."
] | 10.1016/j.isci.2020.101715 | Non-specific | GENE REGULATION | 10.1016/j.isci.2020.101715 | 2,020 | 27 | 0 | iScience | true |
Many plants have a vernalization requirement, that is, they actively repress flowering until after a period of prolonged cold, in order to align seed production with the favourable environmental conditions of spring. Which gene is primarily affected by vernalization in Arabidopsis thaliana, and what is the effect? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"In Arabidopsis thaliana, vernalization involves downregulation and epigenetic silencing of the gene encoding the floral activator FLOWERING LOCUS T (FT).",
"In Arabidopsis thaliana, vernalization involves downregulation and epigenetic silencing of the gene encoding the floral repressor FLOWERING LOCUS C (FLC).",
"In Arabidopsis thaliana, vernalization involves upregulation and epigenetic activation of the gene encoding the floral repressor FLOWERING LOCUS C (FLC)."
] | 10.1146/annurev-cellbio-100616-060546 | Non-specific | GROWTH AND DEVELOPMENT | 10.1146/annurev-cellbio-100616-060546 | 2,017 | 258 | 1 | Annual Review of Cell and Developmental Biology | true |
How does the gene network regulated by the gene FLOWERING LOCUS C (FLC) works in Arabidopsis thaliana to regulate flowering time? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"FLC, a MADS box transcription factor, is a major repressor of flowering in the family Brassicaceae, and it is induced by VERNALIZATION INSENSITIVE3 (VIN3) and VERNALIZATION2 (VRN2). FLC represses the genes FRIGIDA (FRI), the FRI-complex and other genes such us VERNALIZATION INDEPENDENCE3 (VIP3), thereby repressing flowering and setting the requirement for vernalization. When plants are vernalized by winter chilling, FLC is epigenetically repressed, and this is mediated by genes such us FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS D (FD). Consequently, FRI, the FRI-complex and VIP3 expression is derepressed, and flowering is induced.",
"FLC, a MADS box transcription factor, is a major repressor of flowering in the family Brassicaceae, and it is induced by FRIGIDA (FRI), the FRI-complex and other genes such us VERNALIZATION INDEPENDENCE3 (VIP3). FLC represses the floral integrators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS D (FD), thereby delaying flowering and setting the requirement for vernalization. When plants are vernalized by winter chilling, FLC is epigenetically silenced, a process mediated by genes such us VERNALIZATION INSENSITIVE3 (VIN3) and VERNALIZATION2 (VRN2). Consequently, FT, SOC1 and FD expression is derepressed, and flowering is induced.",
"FLC, a MADS box transcription factor, is a major inducer of flowering in the family Brassicaceae, and it is repressed by FRIGIDA (FRI), the FRI-complex and other genes such us VERNALIZATION INDEPENDENCE3 (VIP3). FLC induces the floral integrators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS D (FD), thereby promoting flowering and releasing from the requirement for vernalization. When plants are vernalized by winter chilling, FLC is epigenetically regulated, and this is mediated by genes such us VERNALIZATION INSENSITIVE3 (VIN3) and VERNALIZATION2 (VRN2). Consequently, FT, SOC1 and FD expression is derepressed, and flowering is induced."
] | 10.1111/nph.14520 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/nph.14520 | 2,017 | 37 | 1 | New Phytologist | true |
What is the pleiotropic effect of the gene FLOWERING LOCUS C (FLC) in the life cycle of Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The gene FLOWERING LOCUS C (FLC) act as a pleiotropic gene in the life cycle of Arabidopsis thaliana: it induces flowering and represses germination. The pleiotropic effect depends on the environment experienced by the plants and seeds: mother plants that have experienced vernalization, produced progeny with a lower germination propensity when they have functional FLC and FRIGIDA (FRI) alleles. However, in a functional FRI background, disruption of FLC enhanced the response to maternal vernalization by inducing germination, indicating a positive effect for FRI independently of FLC. This shows slightly convergent pathways in the regulation of flowering and germination.",
"The gene FLOWERING LOCUS D (FD) act as a pleiotropic gene in the life cycle of Arabidopsis thaliana: it represses flowering and induces germination. The pleiotropic effect depends on the environment experienced by the plants and seeds: mother plants that have not experienced summer, produced progeny with a higher germination propensity when they have functional FD, FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) alleles. However, in a functional FD background, disruption of GA20OX1 reduced the response to maternal vernalization by reducing germination, indicating a negative effect for FD independently of SOC1 . This shows slightly divergent pathways in the regulation of flowering and germination.",
"The gene FLOWERING LOCUS C (FLC) act as a pleiotropic gene in the life cycle of Arabidopsis thaliana: it represses flowering and induces germination. The pleiotropic effect depends on the environment experienced by the plants and seeds: mother plants that have not experienced vernalization, produced progeny with a higher germination propensity when they have functional FLC and FRIGIDA (FRI) alleles. However, in a functional FRI background, disruption of FLC reduced the response to maternal vernalization by reducing germination, indicating a negative effect for FRI independently of FLC . This shows slightly divergent pathways in the regulation of flowering and germination."
] | 10.1111/nph.14520 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/nph.14520 | 2,017 | 37 | 2 | New Phytologist | true |
How is FLOWERING LOCUS C (FLC) expression reset during the reproductive stage in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"After fertilization, the repressive effect of vernalization on FLOWERING LOCUS C (FLC) expression is reset in each generation during embryogenesis. Through binding to a distal cis-acting CCAAT at the FLC promoter, the B3-domain transcription factor ABSCISIC ACID INSENSITIVE 5 (ABI5) reactivates FLC expression starting on late embryogenesis up to embryo maturation stages. ABI5 function depends on the binding of the pioneer transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) to a CME motif in the proximal FLC promoter early in the embryogenesis process. Loss of function of ABI3 is related to a reduction of ABI5 binding to the FLC promoter. ABI5 recruits the FRIGIDA (FRI)-complex leading to an increase of the active H3Kme3 and reduction of the H3K27me3 marks on the FLC locus, thereby resetting FLC expression in the seeds.",
"After fertilization, the repressive effect of vernalization on FLOWERING LOCUS C (FLC) expression is reset in each generation during embryogenesis. Through binding to a cis-acting CME at the FLC promoter, the B3-domain transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) reactivates FLC expression starting on late embryogenesis up to embryo maturation stages. ABI3 function depends on the binding of the pioneer transcription factor LEAFY COTYLEDON 1 (LEC1) to a CCAAT motif in the distal FLC promoter early in the embryogenesis process. Loss of function of LEC1 is related to a reduction of ABI3 binding to the FLC promoter. ABI3 recruits the FRIGIDA (FRI)-complex leading to an increase of the active H3Kme3 and reduction of the H3K27me3 marks on the FLC locus, thereby resetting FLC expression in the seeds.",
"After fertilization, the repressive effect of vernalization on FLOWERING LOCUS C (FLC) expression is reinforced in each generation during embryogenesis. Through binding to a cis-acting CME at the FLC promoter, the B3-domain transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) represses FLC expression starting on late embryogenesis up to embryo maturation stages. ABI3 function depends on the binding of the pioneer transcription factor LEAFY COTYLEDON 1 (LEC1) to a CCAAT motif in the distal FLC promoter early in the embryogenesis process. Loss of function of LEC1 is related to an increase of ABI3 binding to the FLC promoter. ABI3 represses the binding of the FRIGIDA (FRI)-complex leading to a reduction of the active H3Kme3 and an increase of the H3K27me3 marks on the FLC locus, thereby repressing FLC expression in the seeds."
] | 10.1093/plcell/koac077 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plcell/koac077 | 2,022 | 25 | 1 | The Plant Cell | true |
How is flowering regulated by vernalization in wheat and barley? | GROWTH AND DEVELOPMENT | [
"Triticum aestivum",
"Hordeum vulgare"
] | [
"VERNALIZATION INDEPENDENCE 1 (VIP1), a B3-domain transcription factor related to the Arabidopsis meristem identity genes VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC), is the main regulator of the response to vernalization in wheat and barley. In spring varieties of these cereals, VIP1 is induced by cold exposure. This induction is epigenetically regulated by the inhibition of the H3K4me3 repressive marks and the promotion of H3K27me3 levels in the VIP1 locus. VIP1 expression is correlated with the down-regulation of VRN2, a repressor of flowering. In consequence, expression of FT (a homolog of Arabidopsis VRN1) is released and flowering is induced.",
"VERNALIZATION1 (VRN1), a MADS box transcription factor related to the Arabidopsis meristem identity genes APETALA1 (AP1) and FRUITFUL (FUL), is the main regulator of the response to photoperiod in wheat and barley. In winter varieties of these cereals, VRN1 is induced by long days. This induction is epigenetically regulated by the inhibition of the H3K27me3 repressive marks and the promotion of H3K4me3 levels in the VRN1 locus. VRN1 expression is correlated with the down-regulation of VRN2 long days, a repressor of flowering. In consequence, expression of VRN3 (a homolog of Arabidopsis FT) is repressed and flowering is induced.",
"VERNALIZATION1 (VRN1), a MADS box transcription factor related to the Arabidopsis meristem identity genes APETALA1 (AP1) and FRUITFUL (FUL), is the main regulator of the response to vernalization in wheat and barley. In winter varieties of these cereals, VRN1 is induced by cold exposure. This induction is epigenetically regulated by the inhibition of the H3K27me3 repressive marks and the promotion of H3K4me3 levels in the VRN1 locus. VRN1 expression is correlated with the down-regulation of VRN2, a repressor of flowering. In consequence, expression of VRN3 (a homolog of Arabidopsis FT) is released and flowering is induced."
] | 10.1111/ppl.13163 | Cereal Grains | GROWTH AND DEVELOPMENT | 10.1111/ppl.13163 | 2,020 | 50 | 2 | Physiologia Plantarum | true |
How does FLOWERING LOCUS T (FT) induces flowering in Arabidopsis plants? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The Arabidopsis FT protein translocates from the source leaves through the phloem to the shoot apex to induce the transition from vegetative to reproductive growth. The FT gene is expressed in the phloem companion cells in source leaves. The protein is then actively translocated to the sieve elements and to the phloem stream through the channel FT INTERACTING PROTEIN 1 (FTIP1). While the load into the phloem occurs through active transport, FT protein unloading into the shoot apical meristem occurs through the function of a passive plasmodesmata pathway not fully understood yet. Once in the shoot apical meristem, FT interacts with FD to transiently induce APETALA1 (AP1) expression, thus leading to floral development.",
"The Arabidopsis FT protein translocates from the source leaves through the phloem to the shoot apex to induce the transition from vegetative to reproductive growth. The FT gene is expressed in the phloem companion cells in source leaves. The protein is then translocated to the xylem elements and to the xylem stream through difussion with the aid of lipids. While the load into the xylem occurs through apoplastic diffusion, FT protein unloading into the shoot apical meristem engages the function of a selective apoplastic pathway not fully understood yet. Once in the shoot apical meristem, FT interacts with AP1 to transiently induce FD expression, thus leading to floral development.",
"The Arabidopsis FT protein translocates from the source leaves through the phloem to the shoot apex to induce the transition from vegetative to reproductive growth. The FT gene is expressed in the phloem companion cells in source leaves. The protein is then translocated to the sieve elements and to the phloem stream through plasmodesmata with the aid of the FT INTERACTING PROTEIN 1 (FTIP1). While the load into the phloem occurs through symplasmic diffusion, FT protein unloading into the shoot apical meristem engages the function of a selective plasmodesmata pathway not fully understood yet. Once in the shoot apical meristem, FT interacts with FD to transiently induce APETALA1 (AP1) expression, thus leading to floral development."
] | 10.1242/dev.171504, 10.1093/pcp/pcae001, 10.1111/tpj.12213 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/tpj.12213 | 2,013 | 79 | 2 | The Plant Journal | true |
What are the number of the overlapping up-regulated genes under heat stress in Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa leaves, and which are the overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species? | ENVIRONMENT - ABIOTIC STRESS | [
"Nothofagus pumilio",
"Arabidopsis thaliana",
"Populus tomentosa"
] | [
"There are at least 68 common-regulated genes between Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa subjected to heat stress. The overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species were: response to unfolded protein, cellular response to unfolded protein, protein refolding, cellular response to topologically incorrect protein, response to topologically incorrect protein, chaperone cofactor-dependent protein refolding, de novo posttranslational protein folding, de novo protein folding, endoplasmic reticulum unfolded protein response, protein folding, chaperone-mediated protein folding, response to heat, cellular response to hypoxia, cellular response to oxygen levels, cellular response to decreased oxygen levels, response to temperature stimulus, response to hypoxia, response to cadmium ion, cellular response to stress, cellular response to chemical stimulus, response to inorganic substance, response to abiotic stimulus, response to organic substance, response to chemical, response to stress.",
"There are at least 68 common-regulated genes between Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa subjected to heat stress. The overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species were: cellular response to unfolded protein, response to unfolded protein, response to topologically incorrect protein, response to stress, response to stimulus, response to organic substance, response to chemical, cellular response to topologically incorrect protein, protein refolding, protein folding, response to cadmium ion, response to metal ion, response to inorganic substance, translation, cellular protein metabolic process. metabolic process, organonitrogen compound metabolic process, organic substance biosynthetic process, biosynthetic process, peptide biosynthetic process, peptide metabolic process, cellular amide metabolic process, organonitrogen compound biosynthetic process, amide biosynthetic process, cellular nitrogen compound biosynthetic process, response to oxidative stress, response to drug, response to salt stress, response to osmotic stress.",
"There are at least 114 common-regulated genes between Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa subjected to heat stress. The overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species were Photosynthesis: light harvesting in photosystem I, photosynthesis: light harvesting, generation of precursor metabolites and energy, photosynthesis: light reaction, photosynthesis: photosynthetic electron transport in photosystem I, photosynthetic electron transport chain, electron transport chain, oxidation-reduction process, protein-chromophore linkage, carbon fixation, gluconeogenesis, glucose metabolic process, hexose metabolic process, monosaccharide metabolic process, hexose biosynthetic process, monosaccharide biosynthetic process, regulation of photosynthesis, light reaction, regulation of photosynthesis, regulation of generation of precursor metabolites and energy, photosystem II assembly, response to high light intensity, response to light intensity, response to light stimulus, response to radiation, response to abiotic stimulus, response to stimulus, response to cytokinin."
] | https://doi.org/10.1371/journal.pone.0246615 | Woody Perennials & Trees | ENVIRONMENT | 10.1371/journal.pone.0246615 | 2,021 | 6 | 0 | PLOS ONE | true |
Which are the over-expressed transcription factor families that showed more than 2-fold enrichment in Nothofagus pumilio leaves under heat stress? | ENVIRONMENT - ABIOTIC STRESS | [
"Nothofagus pumilio"
] | [
"The over-expressed transcription factor families that showed more than 2-fold enrichment in N. pumilio leaves under heat stress HSF1, HSF2, MYB, ERF",
"The over-expressed transcription factor families that showed more than 2-fold enrichment in N. pumilio leaves under heat stress ERF, WRKY, LBD, WOX, EIL.",
"The over-expressed transcription factor families that showed more than 2-fold enrichment in N. pumilio leaves under heat stress ERFs, MYBs, NACs, NF-YC"
] | https://doi.org/10.1371/journal.pone.0246615 | Woody Perennials & Trees | ENVIRONMENT | 10.1371/journal.pone.0246615 | 2,021 | 6 | 1 | PLOS ONE | true |
How is the transcription factors AREB1 involved in the response to drought stress in populus trichocarpa? | ENVIRONMENT - ABIOTIC STRESS | [
"Populus trichocarpa"
] | [
"In Populus trichocarpa, AREB1 binds to ABRE motifs associated with PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, forming AREB1-ADA2b-GCN5 ternary protein complexes. This recruitment enables GCN5-mediated histone acetylation to enhance H3K9ac and increase RNA polymerase II recruitment specifically at these PtrNAC genes for the promotion of drought tolerance. ",
"In Populus trichocarpa, AREB1 binds to ABRE motifs associated with PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, forming AREB1-ADA2b-GCN5 ternary protein complexes. This recruitment disables GCN5-mediated histone acetylation to decrease H3K9ac and increase RNA polymerase II recruitment specifically at these PtrNAC genes for the promotion of drought tolerance. ",
"In Populus trichocarpa, AREB1 binds to ABRE motifs associated with PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, disassembling AREB1-ADA2b-GCN5 ternary protein complexes. This recruitment disables GCN5-mediated histone acetylation to enhance H3K9ac and decrease RNA polymerase II recruitment specifically at these PtrNAC genes for the repression of drought tolerance. "
] | https://doi.org/10.1105/tpc.18.00437 | Woody Perennials & Trees | ENVIRONMENT | 10.1105/tpc.18.00437 | 2,018 | 179 | 0 | The Plant Cell | true |
Which is the effect of warm temperatures on the functioning of the circadian clock and the time-of-day patterns of gene regulation in Nothofagus pumilio leaves under constant conditions? | ENVIRONMENT - ABIOTIC STRESS | [
"Nothofagus pumilio"
] | [
"Warm temperatures affected the functioning of the circadian clock under constant conditions since circadian oscillator components became arrhythmic or showed changes in their moment of maximum expression when seedlings were exposed to 34°C. Warm temperatures also affected the time-of-day patterns of gene regulation, because 72.3% of the differentially expressed genes between subjective dawn and dusk at 20°C lost their regulation at 34°C. ",
"Warm temperatures promoted the functioning of the circadian clock under constant conditions since circadian oscillator components became rhythmic or showed changes in their moment of maximum expression when seedlings were exposed to 34°C. Warm temperatures also affected the time-of-day patterns of gene regulation, because 72.3% of the differentially expressed genes between subjective dawn and dusk at 20°C were up-regulated at 34°C. ",
"Warm temperatures affected the functioning of the circadian clock under constant conditions since circadian oscillator components became arrhythmic or showed changes in their moment of maximum expression when seedlings were exposed to 34°C. Warm temperatures didn’t affect the time-of-day patterns of gene regulation, because only 0.3% of the differentially expressed genes between subjective dawn and dusk at 20°C lost their regulation at 34°C."
] | https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.20342 / https://doi.org/10.1101/2024.03.22.586279 | Woody Perennials & Trees | ENVIRONMENT | 10.1101/2024.03.22.586279 | 2,024 | 0 | 0 | null | true |
Which is the role of STZ1 in the response of abiotic stress in tree species? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"STZ1 is induced by drought, frost, and chilling stress in leaves and promotes the expression of ascorbate peroxidase 2, which promotes the accumulation of ROS and decreases frost tolerance. The ectopic overexpression of STZ1 reduces freezing tolerance in transgenic poplar. ",
"STZ1 is induced by drought, frost, and chilling stress in leaves and promotes the expression of ascorbate peroxidase 2, which scavenges ROS and enhances frost tolerance. The ectopic overexpression of STZ1 improves freezing tolerance in transgenic poplar. ",
"STZ1 is induced by drought, frost, and chilling stress in leaves and represses the expression of ascorbate peroxidase 2, which scavenges ROS and enhances frost tolerance. The ectopic overexpression of STZ1 improves heat tolerance in transgenic poplar."
] | doi: 10.1111/pbi.13130, reviewed in doi:10.1093/jxb/erz532 | Non-specific | ENVIRONMENT | 10.1093/jxb/erz532 | 2,019 | 76 | 1 | Journal of Experimental Botany | true |
What is the distribution pattern of heterochromatic and euchromatic marks at the periphery of tomato nuclei? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"chromatin that carries heterochromatic or euchromatic marks is equally found at the nuclear periphery of tomato nuclei.",
"The chromatin that carries euchromatin marks is highly enriched at the nuclear periphery of tomato nuclei, while heterochromatic marks are depleted. ",
"chromatin that carries heterochromatic marks is highly enriched at the nuclear periphery in tomato nuclei, while euchromatic marks are depleted."
] | 10.1073/pnas.240073712 | Solanaceae & Relatives | GENOME AND GENOMICS | null | null | null | 2 | null | true |
What are the spatial localization patterns of centromeres and telomeres in a plant species with its chromosomes displaying Rabl conformation? | GENOME AND GENOMICS | [
"non-specific"
] | [
"In the Rabl conformation, centromeres are clustered at the nuclear envelope or at one end of the nucleus. The telomeres are evenly distributed in the nucleoplasm.",
"In the Rabl conformation, centromeres are clustered at the nuclear envelope or at one end of the nucleus. The telomeres of the chromosomes are typically found at the opposite end of the nucleus from the centromeres.",
"In the Rabl conformation, centromeres are clustered at the nucleolus. The telomeres are clustered at the nuclear envelope or at one end of the nucleus."
] | 10.1104/pp.111.187161 | Non-specific | GENOME AND GENOMICS | 10.1104/pp.111.187161 | 2,011 | 100 | 1 | Plant Physiology | true |
What changes do telomeres undergo in the Arabidopsis nuc1 mutant? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"The nuc1 mutants exhibit shortened telomeres compared to wild-type Arabidopsis. In addition, telomeres in nuc1 mutants become clustered in the nucleolus.",
"The nuc1 mutants exhibit longer telomeres compared to wild-type Arabidopsis. In addition, compared to wild-type, telomeres in nuc1 mutants are no longer clustered at the nuclear periphery.",
"The nuc1 mutants exhibit shortened telomeres compared to wild-type Arabidopsis. In addition, telomeres in nuc1 mutants are no longer clustered in the nucleolus."
] | 10.1016/j.celrep.2016.07.016 | Model Organisms | GENOME AND GENOMICS | 10.1016/j.celrep.2016.07.016 | 2,016 | 120 | 2 | Cell Reports | true |
How are chromatin accessibility and DNA methylation associated with TADs in Marchantia? | GENOME AND GENOMICS | [
"non-specific"
] | [
"In Marchantia, the TAD borders are depleted of accessible chromatin but enriched with DNA methylation. Moreover, a subset of Marchantia TADs has a high level of chromatin accessibility throughout.",
"In Marchantia, the TAD borders are enriched with accessible chromatin but depleted of DNA methylation. Moreover, a subset of Marchantia TADs has a high level of DNA methylation throughout. ",
"In Marchantia, the TAD borders are enriched with both accessible chromatin and DNA methylation. Moreover, a subset of Marchantia TADs has a high level of DNA methylation and chromatin accessibility throughout."
] | 10.1038/s41477-020-00766-0 | Non-specific | GENOME AND GENOMICS | 10.1038/s41477-020-00766-0 | 2,020 | 66 | 1 | Nature Plants | true |
In Arabidopsis thaliana, how is the expression of TFL1 switched off in floral primordia? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis floral primordia, an enhancer element located at the 3’ downstream region of the TFL1 locus is bound by the MADS-box transcription factor protein complex. Such protein-DNA interaction prevents this cis-element from interacting with the TFL1 transcription start site, ensuring that the expression of TFL1 is turned off.",
"In Arabidopsis floral primordia, an enhancer element located at the 5’ downstream region of the TFL1 locus is bound by the MADS-box transcription factor protein complex. This protein-DNA interaction promotes this cis-element from interacting with the TFL1 transcription termination site, ensuring that the expression of TFL1 is turned off.",
"In Arabidopsis floral primordia, the transcription start site of the TFL1 locus is bound by the MADS-box transcription factor protein complex. Such protein-DNA interaction promotes the TFL1 promoter region to recruit RNA polymerase II, ensuring that the expression of TFL1 is turned off."
] | 10.1016/j.devcel.2013.02.013 | Model Organisms | GENE REGULATION | 10.1016/j.devcel.2013.02.013 | 2,013 | 173 | 0 | Developmental Cell | true |
What are the effects of silicon (Si) application over soybean nodulation and root density in soybean plants and what are the main transcription factors (TFs) families involved in these effects? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Glycine max"
] | [
"Silicon (Si) application increases soybean root development but reduces nodulation. The upregulation of specific TF families such as LysM-RLKs, bHLH, bZIP, MYB, and WRKY, along with the involvement of the cytokinins transporter pathways are involved in these effects. ",
"Silicon (Si) application enhances soybean root development and nodulation. The upregulation of specific TF families such as AP2/ERF-RAV, bHLH, bZIP, MYB, and WRKY, along with the involvement of the auxin transporter pathway are involved in these effects. ",
"Silicon (Si) application reduces soybean root development and nodulation. The upregulation of specific TF families such as AP2/ERF-RAV, bHLH, bZIP, MYB, and WRKY, along with the involvement of the cytokinins transporter pathways are involved in these effects."
] | https://link.springer.com/article/10.1007/s00299-024-03250-7 | Legumes | ENVIRONMENT | 10.1007/s00299-024-03250-7 | 2,024 | 1 | 1 | Plant Cell Reports | true |
Is the non-legume Parasponia andersonii able to control nodule symbiosis in response to exogenous nitrogen concentrations? If so, which symbiotic parameters are affected under high-nitrogen concentrations? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Parasponia andersonii"
] | [
"As well as legumes, the non-legume P. andersonii is able to control nodule symbiosis in response to exogenous nitrogen concentrations. This negative regulation of nodulation is indicated by a reduction in nodule number, total nodule fresh weight, nodule volume and rhizobial CFUs per mg of nodule under low-nitrogen conditions.",
"As well as legumes, the non-legume P. andersonii is able to control nodule symbiosis in response to exogenous nitrogen concentrations. This negative regulation of nodulation is indicated by a reduction in nodule number, total nodule fresh weight, nodule volume and rhizobial CFUs per mg of nodule under high-nitrogen conditions.",
"Unlike legumes, the non-legume P. andersonii is not able to control nodule symbiosis in response to exogenous nitrogen concentrations. This lack of regulation of nodulation is indicated by a similar nodule number, total nodule fresh weight, nodule volume and rhizobial CFUs per mg in low or high nitrogen concentrations."
] | https://doi.org/10.3389/fpls.2019.01779 | Model Organisms | ENVIRONMENT | 10.3389/fpls.2019.01779 | 2,020 | 19 | 1 | Frontiers in Plant Science | true |
What is the impact of nitrogen availability in the soil over Lotus japonicus-Mesorhizobium loti root nodule symbiosis and what are the key genes involved in regulation of nodule number? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Lotus japonicus"
] | [
"Nitrogen availability in the soils positively affects the root nodule symbiosis between Lotus japonicus and Mesorhizobium loti. Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) encodes an NLP (NIN-LIKE PROTEIN) transcription factor that accumulates in the nucleus in response to nitrate and positively affects nodule size and rhizobial infection by controlling the production of the root-derived mobile peptide CLE-RS1 that interacts with HAR-1.",
"Nitrogen availability in the soils negatively affects the root nodule symbiosis between Lotus japonicus and Mesorhizobium loti. Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) encodes an NLP (NIN-LIKE PROTEIN) transcription factor that accumulates in the nucleus in response to nitrate and negatively regulates nodule number by controlling the production of the root-derived mobile peptide CLE-RS2 that interacts with HAR-1.",
"Nitrogen availability in the soils negatively affects the root nodule symbiosis between Lotus japonicus and Mesorhizobium loti. Lotus japonicus NIN encodes a transcription factor that accumulates in the nucleus in response to nitrate and negatively regulates nodule size by controlling the production of the shoot-derived mobile peptide CLE-RS2 that interacts with HAR-1."
] | https://doi.org/10.1038/s41467-018-02831-x | Model Organisms | ENVIRONMENT | 10.1038/s41467-018-02831-x | 2,018 | 146 | 1 | Nature Communications | true |
How does low phosphorus (P) concentration affect root nodule symbiosis in soybean (Glycine max) plants? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Glycine max"
] | [
"Phosphorus (P) is necessary for nitrogen fixation in the root nodules of soybean plants. High phosphorus concentrations negatively affect Nitrogen accumulation, and nodule number, weight and nitrogenase activity. ",
"Phosphorus (P) is necessary for nitrogen fixation in the root nodules of soybean plants. Low phosphorus concentrations negatively affect Nitrogen accumulation, and nodule number, weight and nitrogenase activity. ",
"Phosphorus (P) is not necessary for nitrogen fixation in the root nodules of soybean plants. "
] | https://link.springer.com/article/10.1007/s13199-022-00882-9 | Legumes | ENVIRONMENT | 10.1007/s13199-022-00882-9 | 2,022 | 7 | 1 | Symbiosis | true |
What is the effect of salt stress over the symbiotic signalling pathway in soybean (Glycine max) plants and what are the main genes involved in this effect? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Glycine max"
] | [
"Salt stress inhibits root nodule symbiosis. GmSK2‐8 (glycogen synthase kinase 3‐like kinase) inhibits rhizobial infection and nodule formation in soybean under salt‐stress conditions by phosphorylating the LHR1 domain of GmNSP1a. This phosphorylation inhibits GmNSP1a capability to bind to the promoter region of the symbiotic gene GmERN1a. Additionally, the overexpression of GmSK2‐8 significantly reduces the expression of GmNINb and GmENOD40‐1.",
"Salt stress inhibits root nodule symbiosis. GmSK2‐8 (glycogen synthase kinase 3‐like kinase) inhibits rhizobial infection and nodule formation in soybean under salt‐stress conditions by phosphorylating CCaMK-CYCLOPS. This phosphorylation inhibits their ability to bind to the promoter region of symbiotic genes like GmENOD40‐1.",
"Salt stress promotes root nodule symbiosis by phosphorylating the LHR1 domain of GmNSP1a. This phosphorylation increases GmNSP1a capability to bind to the promoter region of the symbiotic gene GmERN1a. "
] | https://doi.org/10.1016/j.molp.2020.12.015 | Legumes | ENVIRONMENT | 10.1016/j.molp.2020.12.015 | 2,021 | 62 | 0 | Molecular Plant | true |
How post-transcriptional and/or post-translational mechanisms are involved in circadian clock regulation in Arabidopsis thaliana and Drosophila through the action of PROTEIN-ARGININE-METHYL-TRANSFERASE 5? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"PROTEIN METHYL TRANSFERASE5 (PRMT5) methylates clock proteins such as TOC1 in Arabidopsis and PER in flies affecting the activity of these transcription factors that ultimately affect the circadian rhythms in both organisms.",
"PROTEIN METHYL TRANSFERASE5 (PRMT5) methylates several clock proteins leading to degradation. In Arabidopsis TOC1 is methylated in R18 and R20. In Flies, PER is methylated, in this case leading to a more stable protein that looses rhytmicity.",
"PROTEIN METHYL TRANSFERASE5 (PRMT5) regulates the splicing of PRR9 in Arabidopsis and PER in Drosophila melanogaster altering the circadian clock of both organisms. PRMT5 mutants have a wide-variety of splicing defects. PRMT5 methylates several splicing factors and it is the proposed mechanism to have an impact on the splicing pattern."
] | doi: 10.1038/nature09470. and doi: 10.1093/plcell/koae051 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plcell/koae051 | 2,024 | 6 | 2 | The Plant Cell | true |
How does the circadian clock function in individual cells of Arabidopsis? Are all cell types having the same phase of gene expression ? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Arabidopsis exhibits two clock gene expression waves at the plant level: one that travels up the root and one that travels down. Furthermore, the circadian rhythms of the plant's various sections vary slightly; for example, the root's tip has a faster clock. Throughout the plant, strong clock rhythms are also found in individual cells. This robustness may be attributed to clocks in adjacent cells communicating with one another to keep track of time. The two waves of gene expression in the root are explained by mathematical simulations that demonstrate how the interaction of the individual clocks creates patterns of clock activity throughout the plant.\n",
"Light entrains the clock, and therefore tissues that absorb light are the ones that set the time in the whole plant. Still, all parts of the plant show oscillations in gene expression, suggesting a cell-to-cell communication. In roots the clock ticks slower as in leaves, having a period of 25.5 hs instead of 24h. \n\n",
"Clock is entrained by light, therefore, across the whole plant, different cell types have different “clocks” and phase of expression depending on the access to the light source. There is little cell-to-cell communication to coordinate the clock at a whole plant level. Root tissues have weaker oscillations and leaves express genes with higher amplitudes, showing that the clock thought the plant is mainly controlled by the light-absorbing tissues. \n"
] | https://doi.org/10.7554/eLife.31700 | Model Organisms | GROWTH AND DEVELOPMENT | 10.7554/eLife.31700 | 2,018 | 99 | 0 | eLife | true |
Photoperiodic flowering response mechanism can be described by a coincidence model, in which the photoperiodic response is driven by the coincidence of the external light signal and the internal rhythms. In Arabidopsis, which are the main genes that explain this model on photoperiodic flowering and how they are interacting? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Photoreceptors are the main responsibles for photoperiodic flowering. The internal clock controls FKF that induces an increase in CONSTANS mRNA. In the light phase, the CO protein can be activated by PHYTOCHROME B and degradation is promoted by CRYPTOCHROMES and PHYTOCHROME A. High levels of CO protein activate the expression of FLOWERING LOCUS T inducing flowering. ",
"Light entrains the clock but it the case of flowering, it affects the expression of the flowering integrator gene FLOWERING LOCUS T (FT). In Arabidopsis, the FKF1 protein is regulated by the circadian clock and has a diurnal rhythm, accumulating at the middle and end of the day in long days. FKF increases the levels of CONSTANS (CO). In long-days, the CO protein is stabilized by light by the action of the photoreceptors PHYTOCHROME A and CRYPTOCHROMES and can therefore activate FT transcription inducing flowering. In short-days, the CO levels are reached in the dark phase, and in this way no activation of CO protein can occur. \n\n\n",
"Day-length and light plays a minor role in photoperiodic flowering. Light is mainly important for setting the internal clock and controlling the expression of clock genes such as CCA1, TOC1 and PRR7 and PRR9. Disruption of these genes lead to altered flowering. \n"
] | https://doi.org/10.1038/nature00996 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1038/nature00996 | 2,002 | 534 | 1 | Nature | true |
miRNA processing mechanisms differ in plants and animals. Mention two main differences on the miRNA biogenesis pathway that distinguishes these two organism | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"In Plants, miRNA biogenesis takes place exclusively in the nucleus while in animals, the first processing step (first cut of the pri-miRNA to pre-miRNA) takes place in the nucleus and the second cleavage step (from pre-miRNA to mature miRNA) in the cytoplasm. The other difference is that plants pri-miRNA have a much larger heterogeneity at a structural level than the animal's counterpart. This leads to different biogenesis mechanisms. In animal, the dicing steps occur from base to loop of the precursor, while in plants pri-miRNAs can be produced from base to loop, loop to base or in a mixed fashion.",
"In animals, miRNA biogenesis takes place exclusively in the nucleus while in plants, the first processing step (first cut of the pri-miRNA) takes place in the nucleus and the second cleavage step in the cytoplasm. The other difference is that animal miRNAs have a much larger heterogeneity at a structural level than the plants counterpart. \n",
" In animals, miRNA biogenesis takes place exclusively in the nucleus while in plants, the first processing step (first cut of the pri-miRNA to pre-miRNA) takes place in the nucleus and the second cleavage step(from pre-miRNA to mature miRNA) in the cytoplasm. The other difference is that plant miRNAs have a much larger heterogeneity at a structural level than the animals counterpart. This leads to different biogenesis mechanism. In animal, the dicing steps occur from base to loop of the precursor, while in plants pri-miRNAs can be produced from base to loop, loop to base or in a mixed fashion"
] | DOI 10.1016/j.cub.2009.10.072 and 10.1038/emboj.2009.292 | Non-specific | GENE REGULATION | 10.1038/emboj.2009.292 | 2,009 | 171 | 0 | The EMBO Journal | true |
In the circadian timing system, time-of-day-dependent activity of the core oscillator genes involves chromatin-based regulation. How epigenetic mechanisms shape TOC1 rhythmic expression in Arabidopsis thaliana and which are the genes involved. | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Rhythmic expression of TOC1 is achieved by transcriptional and epigenetic mechanisms at its locus. TOC1 levels are maintained low at dusk by the circadian binding of CCA1 to TOC1 promoter . TOC1 mRNA peaking at dawn is preceded by high levels of H3Ac at the TOC1 promoter, a hallmark of active transcription .Following TOC1 peak expression at dawn, transcriptionally silenced chromatin status mediated by histone deacetylase leads to the declining phase of TOC1. \tFurthermore, STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), a component of the FAcilitates Chromatin Transcription (FACT) complex that assists transcription by modulating chromatin structure, associates with the TOC1 promoter following a circadian pattern similar to the TOC1 mRNA oscillation. At the same time, CCA1 binding to the same DNA region leads to a decrease in H3K27me levels, reducing TOC1 expression \n",
"Rhythmic expression of TOC1 is achieved by transcriptional and epigenetic mechanisms at its locus. TOC1 levels are maintained low at dawn by the circadian binding of CCA1 to TOC1 promoter . TOC1 mRNA peaking at dusk is preceded by high levels of H3Ac at the TOC1 promoter, a hallmark of active transcription .Following TOC1 peak expression at dusk, transcriptionally silenced chromatin status mediated by histone deacetylase leads to the declining phase of TOC1. \tFurthermore, STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), a component of the FAcilitates Chromatin Transcription (FACT) complex that assists transcription by modulating chromatin structure, associates with the TOC1 promoter following a circadian pattern similar to the TOC1 mRNA oscillation. At the same time, CCA1 binding to the same DNA region leads to a decrease in H3Ac levels, reducing TOC1 expression \n",
"Rhythmic expression of TOC1 is achieved by transcriptional and epigenetic mechanisms at its locus. TOC1 levels are maintained low at dawn by the circadian binding of CCA1 to TOC1 promoter . TOC1 mRNA peaking at dusk is preceded by high levels of H3K3me at the TOC1 promoter, a hallmark of active transcription .Following TOC1 peak expression at dusk, transcriptionally silenced chromatin status mediated by H3K27me at the locus leads to the declining phase of TOC1. \tFurthermore, STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), a component of the FAcilitates Chromatin Transcription (FACT) complex that assists transcription by modulating chromatin structure, associates with the TOC1 promoter following a circadian pattern similar to the TOC1 mRNA oscillation. At the same time, CCA1 binding to the same DNA region leads to a decrease in H3K4me levels, reducing TOC1 expression.\n"
] | https://doi.org/10.1105/tpc.107.050807, 10.1111/j.1365-313X.2004.02242.x | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/j.1365-313X.2004.02242.x | 2,004 | 69 | 1 | The Plant Journal | true |
How do LSH1 and LSH2 confer symbiotic nodule identity to root cells in Medicago truncatula? | GENE REGULATION - TRANSCRIPTION | [
"Medicago truncatula"
] | [
"LSH1/LSH2 promote cell divisions specifically in the midcortex and control and maintain nodule organ identity, in part through the transcriptional promotion of NOOT1/NOOT2 and NF-YA1, as well as further promoting auxin-cytokinin levels and directly suppressing the lateral root developmental program.",
"LSH1/LSH2 promote cell differentiation specifically in the inner cortex and pericycle and control and maintain nodule organ identity, in part through the transcriptional promotion of NOOT1/NOOT2 and NF-YA1, as well as further promoting auxin-cytokinin levels and directly suppressing the lateral root developmental program.",
"LSH1/LSH2 promote cell divisions specifically in the midcortex and control and maintain nodule organ identity, in part through the transcriptional promotion of NOOT1/NOOT2 and NF-YA1, as well as further promoting auxin-cytokinin levels and directly mimicking the lateral root developmental program."
] | DOI: 10.1111/nph.16950 | Model Organisms | GENE REGULATION | 10.1111/nph.16950 | 2,020 | 40 | 0 | New Phytologist | true |
How do you define a symbiotic island in Medicago truncatula? | GENOME AND GENOMICS | [
"Medicago truncatula"
] | [
"symbiotic islands are genomic clusters of on average 400 kb in length, containing a majority of symbiotically co-regulated genes whose expression is down-regulated in nitrogen-fixing nodules compared to roots. Symbiotic islands in addition display repressive histone marks and DNA methylation patterns and contain numerous expressed non-coding RNAs). Non-coding RNAs and epigenetic regulations are attractive regulatory elements that could explain the coordinated symbiotic expression of genes present on symbiotic islands. ",
"symbiotic islands are genomic clusters of on average 40 kb in length, containing a majority of symbiotically co-regulated genes whose expression is upregulated in nitrogen-fixing nodules compared to roots. Symbiotic islands in addition display differential histone marks and DNA methylation patterns and contain numerous expressed long non-coding RNAs (lncRNAs). LncRNAs and epigenetic regulations are attractive regulatory elements that could explain the coordinated symbiotic expression of genes present on symbiotic islands. ",
"symbiotic islands are genomic clusters of on average 40 kb in length, containing a majority of symbiotically co-regulated genes whose expression is down-regulated in nitrogen-fixing nodules compared to roots. Symbiotic islands in addition display repressive histone marks and DNA methylation patterns and contain numerous expressed long non-coding RNAs (lncRNAs). LncRNAs and epigenetic regulations are attractive regulatory elements that could explain the coordinated symbiotic expression of genes present on symbiotic islands. "
] | doi: 10.1038/s41477-018-0286-7 | Model Organisms | GENOME AND GENOMICS | 10.1038/s41477-018-0286-7 | 2,018 | 231 | 1 | Nature Plants | true |
How does the Nuclear Factor YA1 control nodule development in Medicago truncatula and Lotus japonicus | GENE REGULATION - TRANSCRIPTION | [
"Medicago truncatula",
"Lotus japonicus"
] | [
"NF-YA1 controls cell differentiation during early stages of nodule development by regulating several members of the SHORT INTERNODES/STYLISH (STY) transcription factor gene family in Lotus japonicus but not in Medicago truncatula.\n\n",
"initial symbiotic cell divisions and subsequent nodule emergence, encompassing further cell divisions and nodule patterning, are both regulated by NF-YA1.",
"NF-YA1 controls cell differentiation during early stages of nodule development by regulating several members of the SHORT INTERNODES/STYLISH\n(STY) transcription factor gene family that are known to regulate auxin homeostasis.\nVia this pathway, NF-YA1 regulates determinate (Lotus japonicas) and indeterminate (Medicago truncatula) nodule emergence, encompassing cell divisions leading to nodule patterning, while it does not regulate Initial symbiotic cell divisions leading to nodule primordium formation.\n"
] | doi: 10.1111/nph.16950 | Model Organisms | GENE REGULATION | 10.1111/nph.16950 | 2,020 | 40 | 2 | New Phytologist | true |
What is the difference between determinate and indeterminate nodule development? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Plants that produce determinate nodules require little or no staking while indeterminate nodule producing plants develop into vines that never top off and continue producing until killed by frost.",
"The difference between determinate and indeterminate nodule development lies in the ability of embryonic cells to be committed to specific or general developmental paths. Determinate nodules have predetermined fates and indeterminate nodules do not, allowing the possibility of compensatory development.",
"Indeterminate nodules have a persistent meristem while determinate nodules have a transient meristem. As a result indeterminate nodules are generally elongated while determinate nodules are generally round.The ontogeny of both types of nodules is different: Indeterminate nodules form from inner (nodule primordium and meristem) and central cortical cells (nodule basis) while determinate nodules form from outer cortical cells. Symbiotic bacteria undergo extensive differentiation into nitrogen-fixing bacteroids in indeterminate but not in determinate nodules."
] | non-specific | Non-specific | GROWTH AND DEVELOPMENT | null | null | null | 2 | null | true |
How do you define a pioneer transcription factor (TF)? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"Pioneer transcription factors bind to regulatory transcription factors to control developmental switches.",
"It is a TF that can bind inactive closed and nucleosome occupied chromatin, thereby it increases the accessibility of target sites for other TFs either directly or by recruiting chromatin remodelers iii) As a consequence pioneer TFs control important developmental switches like the vegetative to floral transition in plants.",
"Pioneer transcription factors bind active chromatin regions to silence them.\n"
] | non-specific | Non-specific | GENE REGULATION | null | null | null | 1 | null | true |
What is the role of the SOG1 transcription factor in the Arabidopsis thaliana DNA damage response and what processes its target genes are involved in? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"The MYB3R transcription factor SOG1 is regulated by the DNA damage response. SOG1 promotes cell cycle, programmed cell death, DNA damage, and thereby maintains genome stability. SOG1 indirectly targets and activates dozens of genes involved in DNA damage-associated processes, including transcriptional and posttranscriptional regulation, oxidative stress, defense, cell cycle regulation, cell death, and DNA repair. ",
"The NAC transcription factor SOG1 is a major regulator of the DNA damage response. SOG1 prevents cell cycle arrest, programmed cell death, DNA repair, and thereby maintains genome stability. SOG1 directly targets and represses hundreds of genes involved in DNA damage-associated processes, including transcriptional and posttranscriptional regulation, oxidative stress, defense, cell cycle regulation, cell death, and DNA repair.\n",
"The NAC transcription factor SOG1 is a major regulator of the DNA damage response. SOG1 promotes cell cycle arrest, programmed cell death, DNA repair, and thereby maintains genome stability. SOG1 directly targets and activates hundreds of genes involved in DNA damage-associated processes, including transcriptional and posttranscriptional regulation, oxidative stress, defense, cell cycle regulation, cell death, and DNA repair. "
] | 10.1073/pnas.1810582115 | Model Organisms | GENOME AND GENOMICS | 10.1073/pnas.1810582115 | 2,018 | 128 | 2 | Proceedings of the National Academy of Sciences | true |
In Arabidopsis thaliana, what are the proteins depositing and removing the monoubiquitination of histone H2B and what are the phenotypes of the corresponding mutants? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"The proteins required to monoubiquitinate H2B are the E3 ubiquitin ligases HUB1 and HUB2 and E2 ubiquitin conjugases UBC1, UBC2 and UBC3. The proteins deubiquinating H2B are the ubiquitin-specific proteases UBP22 and UBP26. Mutant plants for HUB1 and HUB2 and UBC1, 2 and 3 are viable with mild phenotypic defects in seed dormancy, cell cycle progression, circadian clock and flowering time control. Mutant plants in UBP22 display no obvious phenotypes while mutants in UBP26 are early flowering and display high rate of seed abortion.",
"The proteins required to monoubiquitinate H2B are the E2 ubiquitin conjugases HUB1 and HUB2 and E3 ubiquitin ligases UBC1, UBC2 and UBC3. The proteins deubiquinating H2B are the ubiquitin-specific proteases UBP22 and UBP26. Mutant plants for HUB1 and HUB2, and UBC1, 2 and 3 are not viable with strong phenotypic defects in seed dormancy, cell cycle progression, circadian clock and flowering time control. Mutant plants in UBP22 display obvious phenotypes while mutants in UBP26 are late flowering and display low rate of seed abortion. \n",
"The proteins required to monoubiquitinate H2B are the E3 ubiquitin ligases HUB1 and HUB2 and E2 ubiquitin conjugases UBC1 UBC2 and UBC3. The proteins deubiquinating H2B are the ubiquitin-specific proteases UBP5, UBP12 and UBP13. Mutant plants for HUB1 and 2 and UBC1, 2 and 3 are viable with mild phenotypic defects in seed germination, cell cycle arrest, circadian clock and flowering time control. Mutant plants in UBP22 display no obvious phenotypes while mutants in UBP26 are early flowering and display high rate of seed germination."
] | 10.7554/eLife.37892 | Model Organisms | GENE REGULATION | 10.7554/eLife.37892 | 2,018 | 74 | 0 | eLife | true |
What chromatin modifications are deposited or removed around a double strand break in Arabidopsis thaliana? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"In arabidopsis thaliana, γH2AX (an H2AX variant phosphorylated on S139), accumulates around double strand breaks through the activity of ATM and ATR kinases. H3K4me2 removal at damaged sites by the LDL1 protein is important for releasing RAD54 during Homologous Recombination. Polymerase-Associated Factor Complex (PAF1C) localize at at double strand breaks and recruits the E2 Ubiquitin-conjugating enzymes UBC1/2 and E3 ligases HUB1/2, which mediate H2B mono-ubiquitination to promote DNA repair through Homologous Recombination. H4K16ac and H2A.Z are also transiently deposited around double strand breaks.\n",
"In arabidopsis thaliana, H2A.Z (an H2A variant), accumulates around double strand breaks through the activity of ATM and ATR phosphatases. H3K4me2 removal at damaged sites by the LDL1 protein is important for recruiting RAD54 during Homologous Recombination. Polymerase-Associated Factor Complex (PAF1C) localize at at double strand breaks and recruits the E2 Ubiquitin-conjugating enzymes UBC1/2 and E3 ligases HUB1/2, which mediate H2B mono-ubiquitination to promote DNA repair through non-homologous end joining. H4K16ac and H2A.Z are also transiently removed around double strand breaks.\n",
"In arabidopsis thaliana, γH2AX (an H2AX variant phosphorylated on S139), is depleted around double strand breaks through the activity of ATM and ATR kinases. H3K4me2 deposition at damaged sites by the LDL1 protein is important for releasing RAD54 during Homologous Recombination. Polymerase-Associated Factor Complex (PAF1C) localize at at double strand breaks and recruits the E2 Ubiquitin-conjugating enzymes UBC1/2 and E3 ligases HUB1/2, which mediate H2B de-ubiquitination to prevent DNA repair through Homologous Recombination. H4K16ac and H2A.Z are also stably deposited around double strand breaks."
] | 10.1038/s41477-024-01678-z | Model Organisms | GENOME AND GENOMICS | 10.1038/s41477-024-01678-z | 2,024 | 1 | 0 | Nature Plants | true |
How UV-induced DNA damage is repaired in Arabidopsis thaliana? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"UV induces DNA breaks, such as cyclobutane pyrimidine dimers (CPDs) and (6–4) pyrimidine-pyrimidone photoproducts. In Arabidopsis thaliana, photoproducts can be repaired by the Direct Repair pathway, a light-independent error-free process catalyzed by DNA photolyase enzymes called PHR1 and UVR3, or by a light-dependent mechanism called the Nucleotide excision repair pathway. Nucleotide excision repair consists in the excision of the damaged DNA strand, followed by homologous recombination.There are two Nucleotide excision repair subpathways: the transcription coupled repair (TCR) pathway which removes DNA damage from actively transcribed genes and the global genome repair pathway which removes damage throughout the genome. ",
"UV induces bulky DNA adducts, such as cyclobutane pyrimidine dimers (CPDs) and (6–4) pyrimidine-pyrimidone photoproducts. In Arabidopsis thaliana, photoproducts can be repaired by the Direct Repair pathway, a light-dependent error-free process catalyzed by DNA photolyase enzymes called PHR1 and UVR3, or by a light-independent mechanism called the Nucleotide excision repair pathway. Nucleotide excision repair consists in the excision of the damaged DNA strand, followed by de novo DNA synthesis.There are two Nucleotide excision repair subpathways: the transcription coupled repair (TCR) pathway which removes DNA damage from actively transcribed genes and the global genome repair pathway which removes damage throughout the genome. ",
"UV induces bulky DNA adducts, such as cyclobutane pyrimidine dimers (CPDs) and (6–4) pyrimidine-pyrimidone photoproducts. In Arabidopsis thaliana, photoproducts can be repaired by the Direct Repair pathway, a light-dependent error-prone process catalyzed by DNA photolyase enzymes called PHR1 and UVR3, or by a light-independent mechanism called the Nucleotide excision repair pathway. Nucleotide excision repair consists in the excision of the damaged DNA strand, followed by de novo DNA synthesis.There are two Nucleotide excision repair subpathways: the transcription coupled repair (TCR) pathway which removes DNA damage from poorly transcribed genes and the global genome repair pathway which removes damage at specific genomic locations. "
] | 10.1371/journal.pgen.1008476 | Model Organisms | GENOME AND GENOMICS | 10.1371/journal.pgen.1008476 | 2,019 | 18 | 1 | PLOS Genetics | true |
What photoreceptors are found in Arabidopsis thaliana plants and what are their subcellular localizations? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Arabidopsis thaliana plants have five classes of photoreceptors. Phytochromes (PHYA-E) perceive red/far-red lights (600–750 nm); cryptochromes (CRY1, CRY2), phototropins (PHOT1 and PHOT2), F-box containing Flavin binding proteins (ZEITLUPE and FKF1/LKP2) perceive blue/UV-A light (320–500 nm); and UVR8 perceive UV-B light (280–320 nm). Phytochromes are localized in the cytosol and translocate to the nucleus upon light activation. CRY1 dually localizes in cytosol and the nucleus while CRY2 is found mainly in the nucleus. Phototropins localize at the plasma membrane and chloroplast outer membrane. ZEITLUPE localizes mainly in the cytoplasm while FKF1/LKP2 mainly in the nucleus. Upon UV-B absorption, the interface between UVR8 dimers breaks, and the resulting monomer migrates into the nucleus.",
"Arabidopsis thaliana plants have five classes of photoreceptors. Phytochromes (PHYA-E) perceive red/far-red lights (600–750 nm); cryptochromes (CRY1, CRY2), phototropins (PHOT1 and PHOT2), F-box containing Flavin binding proteins (ZEITLUPE and FKF1/LKP2) perceive blue/UV-B light (320–500 nm); and UVR8 perceive UV-C light (280–320 nm). Phytochromes are localized in the cytosol and translocate to the nucleus upon dark reversion. CRY2 dually localizes in cytosol and the nucleus while CRY1 is found mainly in the nucleus. Phototropins localize at the plasma membrane and chloroplast outer membrane. ZEITLUPE localizes mainly in the nucleuswhile FKF1/LKP2 mainly in the cytoplasm. Upon UV-B absorption, the interface between UVR8 dimers breaks, and the resulting monomer migrates into the cytosol.\n",
"Arabidopsis thaliana plants have five classes of photoreceptors. Phytochromes (PHYA-E) perceive blue/UV-A light (320–500 nm); cryptochromes (CRY1, CRY2), phototropins (PHOT1 and PHOT2), F-box containing Flavin binding proteins (ZEITLUPE and FKF1/LKP2) perceive red/far-red lights (600–750 nm); and UVR8 perceive UV-B light (280–320 nm). Phytochromes are localized in the nucleus and translocate to the cytosol upon light activation. CRY1 dually localizes in cytosol and the nucleus while CRY2 is found mainly in the cytosol. Phototropins localize at the plasma membrane and chloroplast inner membrane. ZEITLUPE localizes mainly in the cytoplasm while FKF1/LKP2 mainly in the nucleus. Upon UV-B absorption, UVR8 dimers form and migrate into the nucleus."
] | 10.1016/j.semcdb.2019.03.007 and 10.1016/B978-0-12-801922-1.00009-9 and 10.1093/mp/sss007 and 10.1111/nph.18007 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/nph.18007 | 2,022 | 27 | 0 | New Phytologist | true |
Which proteins reside in siRNA-bodies of Arabidopsis thaliana cells and what is the impact of depleting these proteins? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"siRNA-bodies contain AGO1, AGO7, RDR2, SGS3. Depleting AGO7, RDR6, SGS3 impact the production of TAS3 tasiRNAs, while depleting AGO1, RDR6, SGS3 impact the production of TAS1 and TAS2 tasiRNAs as well as the production of secondary siRNAs involved in the amplification of transgene PTGS ",
"siRNA-bodies contain AGO1, AGO7, RDR6, SGS3. Depleting AGO7, RDR6, SGS3 impact the production of TAS3 tasiRNAs, while depleting AGO1, RDR6, SGS3 impact the production of TAS1 and TAS2 tasiRNAs as well as the production of secondary siRNAs involved in the amplification of transgene PTGS",
"siRNA-bodies contain AGO1, AGO7, RDR6, SDE3. Depleting AGO7, RDR6, SGS3 impact the production of TAS3 tasiRNAs, while depleting AGO1, RDR6, SGS3 impact the production of TAS1 and TAS2 tasiRNAs as well as the production of secondary siRNAs involved in the amplification of transgene PTGS "
] | non-specific | Model Organisms | GENE REGULATION | null | null | null | 1 | null | true |
What type of RNA binds to the plant protein SUPPRESSOR OF GENE SILENCING 3 (SGS3)? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"SGS3 binds to single-stranded RNA",
"SGS3 binds to double-stranded RNA with long 3’ overhang",
"SGS3 binds to double-stranded RNA with long 5’ overhang"
] | non-specific | Model Organisms | GENE REGULATION | null | null | null | 2 | null | true |
What are the functions of plant DICER-LIKE 2 (DCL2) and DCL4, and what is the relationship between these two enzymes? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"DCL2 produces 21-nt siRNAs whereas DCL4 produces 22-nt siRNAs. Their functions are redundant.",
"DCL2 produces 22-nt siRNAs whereas DCL4 produces 21-nt siRNAs. Their functions are either redundant, synergistic or antagonistic, depending on the target considered",
"DCL2 produces 21-nt siRNAs whereas DCL4 produces 22-nt siRNAs. Their functions are antagonistic"
] | non-specific | Non-specific | GENE REGULATION | null | null | null | 1 | null | true |
What is the function of plant ARGONAUTE 1 (AGO1), and what is the phenotype of Arabidopsis thaliana ago1 mutants ? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"AGO1 binds to miRNA and siRNA with a 5’U, and catalyze the cleavage of mRNA homologous to the miRNA and siRNA bound to AGO1. Hypomorphic ago1 alleles are fertile while ago1 nul alleles are dwarf and sterile. ",
"AGO1 binds to miRNA and siRNA with a 5’A, and catalyze the cleavage of mRNA homologous to the miRNA and siRNA bound to AGO1. Hypomorphic ago1 alleles are fertile while ago1 nul alleles are dwarf and sterile. ",
"AGO1 binds to miRNA but not siRNA, and catalyze the cleavage of mRNA homologous to the miRNA and siRNA bound to AGO1. Hypomorphic ago1 alleles are fertile while ago1 nul alleles are dwarf and sterile. "
] | non-specific | Non-specific | GENE REGULATION | null | null | null | 0 | null | true |
What is the function of the protein JUMONJI14 (JMJ14) in plants and what are the consequences of JMJ14 impairment on chromatin? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"non-specific"
] | [
"JMJ14 encodes a the H3K4me3 methylase. JMJ14 impairment increase the level of H3K4me3 but does not modify DNA methylation, except at transgenes.",
"JMJ14 encodes a the H3K9me3 demethylase. JMJ14 impairment increase the level of H3K4me9 but does not modify DNA methylation, except at transgenes.",
"JMJ14 encodes a the H3K4me3 demethylase. JMJ14 impairment increase the level of H3K4me3 but does not modify DNA methylation, except at transgenes."
] | non-specific | Non-specific | GENE REGULATION | null | null | null | 2 | null | true |
In Arabidopsis thaliana, light regulates alternative splicing of RS31. How does light quality and quantity affect this regulation of alternative splicing? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Arabidopsis thaliana plants are exposed to light and darkness. In the presence of light, the splicing index of RS31 decreases. Changes in RS31 alternative splicing are proportional to light quantity (light intensity): plants exposed to higher light intensities show a lower splicing index. Regarding light quality, both red (660 nm) and blue (470 nm) lights produce similar results as white light.",
"Arabidopsis thaliana plants are exposed to light and darkness. In the presence of light, the splicing index of RS31 increases. Changes in RS31 alternative splicing are proportional to light quantity (light intensity): plants exposed to higher light intensities show higher splicing index. Regarding light quality, red (660 nm) does not affect the splicing index but blue (470 nm) light produces similar results as white light.",
"Arabidopsis thaliana plants are exposed to light and darkness. In the presence of light, the splicing index of RS31 increases. Changes in RS31 alternative splicing are not proportional to light quantity (light intensity): plants exposed to different light intensities show the same splicing index. Regarding light quality, both red (660 nm) and blue (470 nm) lights produce similar results as white light."
] | 10.1126/science.1250322 | Model Organisms | ENVIRONMENT | 10.1126/science.1250322 | 2,014 | 179 | 0 | Science | true |
What is the light photosensory pathway that regulates RS31 alternative splicing in Arabidopsis thaliana? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"RS31 alternative splicing responses to light/dark are affected in phytochrome and cryptochrome signaling mutants. Light sensed by phytochromes produces the light effect on alternative splicing. When plants are exposed to light, a phytochrome signal is generated in the photosynthetic tissue and travels through the plant. The mobile signal generated in the leaves triggers root alternative splicing changes in responses to light.",
"RS31 alternative splicing responses to light/dark are not affected in phytochrome and cryptochrome signaling mutants ruling out this photosensory pathway in this light regulation. Light is sensed by the chloroplast. When plants are exposed to light, a chloroplast retrograde signal is generated in the photosynthetic tissue and travels through the plant. The mobile signal generated in the leaves triggers root alternative splicing changes in responses to light.",
"RS31 alternative splicing responses to light/dark are not affected in phytochrome and cryptochrome signaling mutants ruling out this photosensory pathway in this light regulation. Light is sensed by the chloroplast. When plants are exposed to light, a chloroplast retrograde signal is generated in the photosynthetic tissue. The light effect on alternative splicing is only observed in photosynthetic tissues. There are no changes in roots: alternative splicing changes in responses to light only affect leaves."
] | 10.1126/science.1250322 | Model Organisms | ENVIRONMENT | 10.1126/science.1250322 | 2,014 | 179 | 1 | Science | true |
What is the impact of RNA Pol II elongation in the regulation of alternative splicing by light in Arabidopsis thaliana? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the effect of light on alternative splicing is not affected in a dominant negative mutant of the transcription elongation factor TFIIS (that shows defective growth and serrated leaves and general splicing defects compared to wild-type plants). In the tfiis mutant, the differences in the splicing index of RS31 or U2AF65 upon light-dark changes are are similar to wild type plants. Furthermore, trichostatin A, a drug that inhibits histone acetylation, mimics the effect of darkness on alternative splicing. When RNA Pol II elongation is genetically affected, the effect of light on alternative splicing does not change, which discards the possibility that light regulates alternative splicing by controlling plant transcriptional elongation.",
"In Arabidopsis thaliana, the effect of light on alternative splicing is not affected in a dominant negative mutant of the transcription elongation factor TFIIS (that shows defective growth and serrated leaves and general splicing defects compared to wild-type plants). In the tfiis mutant, the differences in the splicing index of RS31 or U2AF65 upon light-dark changes are similar to wild type plants. Furthermore, camptothecin, a topoisomerase inhibitor that also inhibits RNA Pol II elongation decreases the splicing index of RS31, mimicking, therefore, the effects of light. When RNA Pol II elongation is inhibited by a drug the effect of light on alternative splicing is enhanced, which suggests the possibility that light regulates alternative splicing by controlling plant transcriptional elongation.",
"In Arabidopsis thaliana, the effect of light on alternative splicing is abolished in a dominant negative mutant of the transcription elongation factor TFIIS (that shows defective growth and serrated leaves and general splicing defects compared to wild-type plants). In the tfiis mutant, the differences in the splicing index of RS31 or U2AF65 upon light-dark changes are completely abolished. Furthermore, camptothecin, a topoisomerase inhibitor that also inhibits RNA Pol II elongation increases the splicing index of RS31, mimicking, therefore, the effects of darkness. When RNA Pol II elongation is inhibited by a drug or genetically affected, the effect of light on alternative splicing is reduced or abolished, which strengthens the possibility that light regulates alternative splicing by controlling plant transcriptional elongation."
] | 10.1016/j.molcel.2018.12.005 | Model Organisms | ENVIRONMENT | 10.1016/j.molcel.2018.12.005 | 2,019 | 88 | 2 | Molecular Cell | true |
In Arabidopsis thaliana, which is the signaling molecule that regulates alternative splicing by light in roots? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Light regulates alternative splicing in Arabidopsis thaliana. Light-induced changes in alternative splicing in roots occur even if communication with the photosynthetic tissue is interrupted. Small RNAs modulate nuclear alternative splicing of RS31 and other genes, especially in root cells. Small RNAs produced in photosynthetic cells are the main drivers of light-regulated alternative splicing in non-photosynthetic cells.",
"Light regulates alternative splicing in Arabidopsis thaliana. Light-induced changes in alternative splicing in roots only occur as long as communication with the photosynthetic tissue is not interrupted. Small RNAs modulate nuclear alternative splicing of RS31 and other genes, especially in root cells. Small RNAs produced in photosynthetic cells are the main drivers of light-regulated alternative splicing in non-photosynthetic cells.",
"Light regulates alternative splicing in Arabidopsis thaliana. Light-induced changes in alternative splicing in roots only occur as long as communication with the photosynthetic tissue is not interrupted. Sucrose modulates nuclear alternative splicing of RS31 and other genes, especially in root cells. Sugars produced in photosynthetic cells are the main drivers of light-regulated alternative splicing in non-photosynthetic cells."
] | 10.1016/j.celrep.2021.109676 | Model Organisms | ENVIRONMENT | 10.1016/j.celrep.2021.109676 | 2,021 | 42 | 2 | Cell Reports | true |
In Arabidopsis thaliana, what is the regulation of alternative splicing by light in leaves and roots? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"In leaves, light is initially sensed by phytochromes and cryptochromes and activates photosynthesis. Then synthesized sugars are loaded into the phloem and travel to non-photosynthetic root tissues. There, imported sugars are metabolized through glycolysis, producing pyruvate that enters the mitochondria. Oxidative phosphorylation in the mitochondria activates HXK1 kinase and, in turn, modulates alternative splicing outcomes in roots.\nIn leaves, TOR kinase does not participate in the regulation of nuclear alternative splicing: there are other retrograde signals derived from the photosynthetic electron transport that modulate nuclear splicing decisions.",
"In leaves, light is initially sensed by the chloroplast and activates photosynthesis. Then small RNAs are loaded into the phloem and travel to non-photosynthetic root tissues. There, imported sugars are metabolized through glycolysis, producing pyruvate that enters the mitochondria. Imported sugars and small RNAs in the mitochondria activates TOR kinase and, in turn, modulates alternative splicing outcomes in roots.\nIn leaves, even though mitochondria and TOR kinase regulate nuclear alternative splicing, there are other retrograde signals derived from the photosynthetic electron transport that can modulate nuclear splicing decisions.",
"In leaves, light is initially sensed by the chloroplast and activates photosynthesis. Then synthesized sugars are loaded into the phloem and travel to non-photosynthetic root tissues. There, imported sugars are metabolized through glycolysis, producing pyruvate that enters the mitochondria. Oxidative phosphorylation in the mitochondria activates TOR kinase and, in turn, modulates alternative splicing outcomes in roots.\nIn leaves, even though mitochondria and TOR kinase regulate nuclear alternative splicing, there are other retrograde signals derived from the photosynthetic electron transport that can modulate nuclear splicing decisions."
] | 10.1016/j.celrep.2021.109676 | Model Organisms | ENVIRONMENT | 10.1016/j.celrep.2021.109676 | 2,021 | 42 | 2 | Cell Reports | true |
What is the effect of nitrogen (N) on the control of flowering time in Arabidopsis thaliana and what are the key genes involved in this process? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"While low N concentrations delay flowering time, Arabidopsis plants grown under high N accelerate flowering time. N regulates the expression of flowering-related genes at the shoot apical meristem (SAM) to modulate flowering time; these genes include SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), VERNALIZATION 2 (VRN2), and FLOWERING LOCUS T (FT).",
"While high N concentrations delay flowering time, Arabidopsis plants grown under low N accelerate flowering time. N regulates the expression of flowering-related genes at the shoot apical meristem (SAM) to modulate flowering time; these genes include SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), VERNALIZATION 2 (VRN2), and FLOWERING LOCUS T (FT),",
"While high N concentrations delay flowering time, Arabidopsis plants grown under low N accelerate flowering time. On the other hand, extreme N deficiency delay flowering time. N regulates the expression of flowering-related genes at the shoot apical meristem (SAM) to modulate flowering time; these genes include SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), CONSTANS (CO) and FLOWERING LOCUS T (FT)."
] | doi: 10.3390/ijms25105310 | Model Organisms | GROWTH AND DEVELOPMENT | 10.3390/ijms25105310 | 2,024 | 0 | 2 | International Journal of Molecular Sciences | true |
What is the cellular mechanism involved in the growth of the hypocotyl in Arabidopsis thaliana? What are the hormonal pathways participating in this process? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The growth of the hypocotyl in Arabidopsis seedlings is the result of regulated cell division by several factors, including plant hormones. Gibberellin (GA), ethylene, and auxin are plant hormones that promote hypocotyl elongation in Arabidopsis seedlings.",
"The growth of the hypocotyl in Arabidopsis seedlings is the result of regulated cell expansion by several factors, including plant hormones. Gibberellin (GA), ethylene, and auxin are plant hormones that promote hypocotyl elongation in Arabidopsis seedlings.",
"The growth of the hypocotyl in Arabidopsis seedlings is the result of regulated cell division and expansion by several factors, including plant hormones. Gibberellin (GA), cytokinin, and auxin are plant hormones that promote hypocotyl elongation in Arabidopsis seedlings."
] | doi: 10.1104/pp.114.1.295. | Model Organisms | GROWTH AND DEVELOPMENT | 10.1104/pp.114.1.295 | 1,997 | 516 | 1 | Plant Physiology | true |
What is the impact of Nitrate (N) in Arabidopsis thaliana auxin homeostasis during lateral root development and what are the key genes involved in this process? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Auxin perception and nitrate signaling are closely interconnected. Nitrate induces transcription of the ARF8 auxin receptor gene, while N metabolites produced by nitrate reduction and assimilation reset AFB3 levels over time by posttranscriptional regulation via miR167. Downstream of ARF8, a pericycle regulatory mechanism involving IAA14 and the NAC4 and OBP4 transcription factors induces LR initiation and elongation in response to nitrate resupply of N-deficient roots.",
"Auxin perception and nitrate signaling are closely interconnected. Nitrate induces transcription of the AFB3 auxin receptor gene, while N metabolites produced by nitrate reduction and assimilation reset AFB3 levels over time by posttranscriptional regulation via miR393. Downstream of AFB3, a pericycle regulatory mechanism involving IAA14 and the NAC4 and OBP4 transcription factors induces LR initiation and elongation in response to nitrate resupply of N-deficient roots.",
"Auxin perception and nitrate signaling are closely interconnected. Nitrate represses transcription of the AFB3 auxin receptor gene, while N metabolites produced by nitrate reduction and assimilation reset AFB3 levels over time by posttranscriptional regulation via miR393. Downstream of AFB3, a pericycle regulatory mechanism involving IAA14 and the NAC4 and OBP4 transcription factors represses LR initiation and elongation in response to nitrate resupply of N-deficient roots."
] | https://doi.org/10.1073/pnas.1310937110 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1073/pnas.1310937110 | 2,013 | 178 | 1 | Proceedings of the National Academy of Sciences | true |
What is the effect of nitrogen on the root hair development in Arabidopsis thaliana and what are the key genes involved in this process? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, ammonium is able to stimulate root hair initiation. In response to nitrate, NRT1.1 transceptor and TGA1/TGA4 transcription factor regulates expression of the CPC root hair cell specification gene affecting root hair density.",
"In Arabidopsis thaliana, nitrate and not a product of nitrate reduction is able to stimulate root hair initiation. In response to nitrate, NRT1.1 transceptor and TGA1/TGA4 transcription factor regulates expression of the CPC root hair cell specification gene affecting root hair density.",
"In Arabidopsis thaliana, nitrate and other N metabolite are able to stimulate root hair initiation. In response to nitrogen, NRT1.1 transceptor and TGA2/TGA7 transcription factor regulates expression of the CPC root hair cell specification gene affecting root hair density."
] | https://doi.org/10.1111/tpj.13656 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/tpj.13656 | 2,017 | 102 | 1 | The Plant Journal | true |
How are the transcription factors TGA involved in the nitrate response of Arabidopsis thaliana roots? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, all TGAs transcription factors have a role in root nitrate responses. Expression of TGAs is induced downstream of AtNRT1.1 with external nitrate application. TGAs directly bind to the promoter of AtNRT2.1/2.2 and promote the expression of NRT2.1/2.2 Mutations TGAs1 inhibit LR initiation, emergence, root hair initiation, and primary root length. ",
"In Arabidopsis thaliana, TGA1 and TGA4 transcription factors, but not other TGA members, have a role in root nitrate responses. Expression of both TGA1 and TGA4 is repressed downstream of AtNRT1.1 with external nitrate application. TGA1 could directly bind to the promoter of AtNRT2.1/2.2 and repressed the expression of NRT2.1/2.2. Mutations of both TGA1 and TGA4 induced LR initiation, emergence, root hair initiation, and primary root length.",
"In Arabidopsis thaliana, TGA1 and TGA4 transcription factors, but not other TGA members, have a role in root nitrate responses. Expression of both TGA1 and TGA4 is induced downstream of AtNRT1.1 with external nitrate application. TGA1 directly bind to the promoter of AtNRT2.1/2.2 and promote the expression of NRT2.1/2.2. Mutations of both TGA1 and TGA4 inhibit LR initiation, emergence, root hair initiation, and primary root length. "
] | doi: 10.1111/tpj.12618. | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/tpj.12618 | 2,014 | 252 | 2 | The Plant Journal | true |
Which genes encoding transcription factors have been identified as bona fide direct targets of the Arabidopsis thaliana transcription factor BRC1? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"HD-Zip genes HB21, HB40 and HB53; bZIP genes GBF2, GBF3, ABF3 and ABI5; NAC genes ATAF1 and NAC032; AP2/EREB genes ERF113/Rap2.6L and CRF6; MYB genes MYBC1, and MYBD; zinc finger protein gene ATTZF5; and heat shock protein gene HSB2A ",
"HD-Zip gene HB2; bZIP gene bZIP43 and bZIP23, NAC gene NAC019; AP2/EREB genes RAP2.1 and RAP2.12; MYB genes MYB116 and MYB93; zinc finger protein gene SOM and TT1; and heat shock protein gene HSP21",
"HD-Zip genes HB4; bZIP genes DPBF2 and BZIP61; NAC genes NAC097 and NAC058; AP2/EREB genes RAP2.7 and RAP2.9; MYB genes MYB122 and MYB100; zinc finger protein gene BBX26 and DAZ1; and heat shock protein gene HSFA6B"
] | doi: 10.1111/nph.19420 | Model Organisms | GENE REGULATION | 10.1111/nph.19420 | 2,023 | 14 | 0 | New Phytologist | true |
What is the role of the TCP transcription factor BRANCHED1 in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"BRC1 acts systemically across the plant as an integrator of signals controlling bud outgrowth and translates them into a response of cell growth arrest",
"BRC1 acts systemically across the plant as an integrator of signals promoting bud outgrowth and translates them into a response of cell division and growth ",
"BRC1 acts locally inside the buds as an integrator of signals suppressing bud outgrowth and translates them into a response of cell growth arrest."
] | www.plantcell.org/cgi/doi/10.1105/tpc.106.048934 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1105/tpc.106.048934 | 2,007 | 686 | 2 | The Plant Cell | true |
Which protein acts as the receptor of strigolactones in Arabidopsis thaliana? | HORMONES | [
"Arabidopsis thaliana"
] | [
"The receptor of strigolactones in Arabidopsis thaliana is GAI, AT3G03990. ",
"The receptor of strigolactones in Arabidopsis thaliana is KAI2, AT3G03990. ",
"The receptor of strigolactones in Arabidopsis thaliana is AtD14, D14, AT3G03990. \n\n"
] | www.plantcell.org/cgi/doi/10.1105/tpc.114.122903 | Model Organisms | HORMONES | 10.1105/tpc.114.122903 | 2,014 | 193 | 2 | The Plant Cell | true |
Which hormone accumulates in Arabidopsis thaliana dormant axillary buds in response to the activity of BRANCHED1? | HORMONES | [
"Arabidopsis thaliana"
] | [
"Abscisic acid (ABA) accumulates in dormant axillary buds in response to the activity of BRANCHED1 ",
"Salicylic acid accumulates in dormant axillary buds in response to the activity of BRANCHED1 ",
"Gibberellins accumulates in dormant axillary buds in response to the activity of BRANCHED1 "
] | www.pnas.org/cgi/doi/10.1073/pnas.1613199114 | Model Organisms | HORMONES | 10.1073/pnas.1613199114 | 2,016 | 220 | 0 | Proceedings of the National Academy of Sciences | true |
What is the role of StBRANCHED1b of Solanum tuberosum | GROWTH AND DEVELOPMENT | [
"Solanum tuberosum"
] | [
"In Solanum tuberosum BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This increases sucrose accumulation and block the access of the tuberigen protein SP6A. BRC1b also directly interacts with SP5G and induces its tuber-inducing activity in aerial nodes. Altogether, these actions prevent tuberization underground.",
"In Solanum tuberosum BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground.",
"In Solanum tuberosum BRC1b promotes axillary bud activity, auxin responses and an increased number of plasmodesmata in buds. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground."
] | https://doi.org/10.1038/s41477-022-01112-2 | Solanaceae & Relatives | GROWTH AND DEVELOPMENT | 10.1038/s41477-022-01112-2 | 2,022 | 56 | 1 | Nature Plants | true |
Which are the main proteins involved in plant miRNA processing? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"miRNA processing is mediated by DICER-LIKE1 (DCL1) assisted by the dsRNA-binding (DRB) proteins HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE). While DCL1 is an RNAseIII proteins producing the RNA cleavage, both HYL1 and SE facilitate accurate processing of pri-miRNAs by DCL1",
"miRNA processing is mediated by HYPONASTIC LEAVES 1 (HYL1) assisted by DICER-LIKE1 (DCL1) and SERRATE (SE). While HYL1 is an RNAseIII proteins producing the RNA cleavage, both DCL1 and SE facilitate accurate processing of pri-miRNAs by DCL1",
"miRNA processing is mediated by ARGONAUTE1 (AGO1) assisted by the dsRNA-binding (DRB) proteins HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE). While AGO1 is an RNAseIII proteins producing the RNA cleavage, both HYL1 and SE facilitate accurate processing of pri-miRNAs by DCL1"
] | https://doi.org/10.1146/annurev-arplant-050213-035728 | Non-specific | GENE REGULATION | 10.1146/annurev-arplant-050213-035728 | 2,014 | 501 | 0 | Annual Review of Plant Biology | true |
Where does the miRNA biogenesis take place in plants? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"The dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) associate with DCL1 to form nuclear dicing bodies (D-bodies), where miRNA biogenesis take place.",
"The dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) associate with DCL1 to form cytoplasmic processing bodies (P-bodies), where miRNA biogenesis take place.",
"The dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) associate with DCL1 to form cytoplasmic dicing bodies (D-bodies), where miRNA biogenesis take place."
] | https://doi.org/10.1146/annurev-arplant-050213-035728 | Non-specific | GENE REGULATION | 10.1146/annurev-arplant-050213-035728 | 2,014 | 501 | 0 | Annual Review of Plant Biology | true |
How many mechanisms of miRNA biogenesis have been described in plants? Describe them. | GENE REGULATION - PTGS | [
"non-specific"
] | [
"Plant pre-miRNAs are much more variable in length than their ∼70-nt metazoan counterparts (ranging from 49 to 900 nt in length) and can undergo two main processing mechanisms, influenced by the number of cuts required for miRNA release: Short base-to-loop, Sequential base-to-loop.",
"Plant pre-miRNAs are much more variable in length than their ∼70-nt metazoan counterparts (ranging from 49 to 900 nt in length) and can undergo four main processing mechanisms, influenced by the sequential processing direction and number of cuts required for miRNA release: Short base-to-loop, Sequential base-to-loop, Short loop-to-base, and Sequential loop-to-base.",
"As ocurr with metazoan counterparts, plant miRNAs precusrsor are ∼70-nt lenght and undergo one processing mechanisms that consist in two cleavage in a base-to-loop direction."
] | https://doi.org/10.1146/annurev-arplant-050213-035728 | Non-specific | GENE REGULATION | 10.1146/annurev-arplant-050213-035728 | 2,014 | 501 | 1 | Annual Review of Plant Biology | true |
Which are the main determinants during miRNA biogenesis in plants? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"The stem-loop structure contained within miRNAs primary transcripts defines the miRNA precursor. Sequences determinants initiate at least two staggered cleavage events within the pre-miRNA stem, separated by approximately 21 nt, which release the miRNA and its opposing fragment (miRNA∗). The second cut is also determine in sequence dependent manner. ",
"The stem-loop structure contained within miRNAs primary transcripts defines the miRNA precursor. There are not clear determinants which initiate the cleavage events.",
"The stem-loop structure contained within miRNAs primary transcripts defines the miRNA precursor. Structural determinants initiate at least two staggered cleavage events within the pre-miRNA stem, separated by approximately 21 nt, which release the miRNA and its opposing fragment (miRNA∗). Of key importance is the first cleavage position, which determines the mature miRNA sequence and therefore its target specificity. The second cut usually proceeds at a fixed distance from the end of the precursor."
] | https://doi.org/10.1146/annurev-arplant-050213-035728 | Non-specific | GENE REGULATION | 10.1146/annurev-arplant-050213-035728 | 2,014 | 501 | 2 | Annual Review of Plant Biology | true |
Is miRNA biogenesis and miRNA AGO1 nuclear loading connected in Arabidopsis thaliana? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"Yes, there is evidence of DCL1 and AGO1 interaction in the nucleus of plant cell.",
"While miRNA biogenesis has been described linked to AGO miRNA loading in animals, is it not clear the connection between miRNA biogenesis and miRNA AGO1 nuclear loading in plants.",
"Yes, AGO1 is essential during miRNA biogenesis in plants."
] | https://doi.org/10.1016/j.molcel.2018.01.007 | Non-specific | GENE REGULATION | 10.1016/j.molcel.2018.01.007 | 2,018 | 209 | 1 | Molecular Cell | true |
What is the impact of low levels of nitrates in Arabidopsis thaliana during root hair development and what are the key genes involved in this process? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"High nitrogen enhances auxin accumulation in the lateral roots via the repression of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8. Auxin is then accumulated in the root tip by the auxin transport system, namely AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon entering the lateral roots, auxin represses the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6/8) to decrease the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to direct lateral root growth in response to high nitrogen levels.",
"Low nitrogen enhances auxin accumulation in the root apex via the overexpression of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8. Auxin is then transported to the root hair differentiation zone by the auxin transport system, namely AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon entering the RH zone, auxin activates the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6/8) to enhance the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to direct RH elongation in response to low nitrogen levels.",
"High nitrogen enhances auxin accumulation in the root apex via the repression of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8. Auxin is then transported to the atrichoblast cells by the auxin transport system, namely AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon entering the RH zone, auxin represses the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6/8) to decrease the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to direct RH elongation in response to high nitrogen levels."
] | Jia Z, Giehl RFH, Hartmann A, Estevez JM, Bennett MJ, von Wirén N. A spatially concerted epidermal auxin signaling framework steers the root hair foraging response under low nitrogen. Curr Biol. 2023 Sep 25;33(18):3926-3941.e5. doi:10.1016/j.cub.2023.08.040. | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.cub.2023.08.040 | 2,023 | 27 | 1 | Current Biology | true |
How receptor FERONIA and TOR kinase pathway control in Arabidopsis thaliana root hair growth under low temperature condition? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Low temperature (10°C) induce a significant RH elongation response in Arabidopsis thaliana via FERONIA and TOR kinase pathway. FERONIA is essential for detecting restricted nutrition availability resulting from low temperatures. FERONIA interacts with and activates TOR kinase downstream components to trigger RH growth. Moreover, the small GTPase Rho of plants 2 (ROP2) participates in the RH growth response, connecting FER and TOR. We discovered that restricted nitrogen nutrient availability may replicate the RH growth response at 10°C in a way reliant on NRT1.1. ",
"Low temperature (10°C) induce a repression of the RH elongation response in Arabidopsis thaliana via FERONIA and TOR kinase pathway. FERONIA is essential for detecting high levels of nutrition availability resulting from low temperatures. FERONIA interacts with and represses TOR kinase downstream components to inhibit RH growth. Moreover, the small GTPase Rho of plants 2 (ROP2) blocks the RH growth response, repressing FER and TOR. We discovered that high levels of nitrogen nutrient availability may replicate the RH growth response at 10°C independently of NRT1.1.",
"Low temperature (10°C) induce a repression of the lateral root elongation response in Arabidopsis thaliana via FERONIA and TOR kinase pathway. FERONIA is essential for detecting high levels of nutrition availability resulting from low temperatures. FERONIA do not interact with and release TOR kinase downstream components to repress lateral roots growth. Moreover, the small GTPase Rho of plants 2 (ROP2) locates on the root tips, repressing FER and TOR. We discovered that high levels of nitrogen nutrient availability may replicate the lateral root growth response at 10°C independently of NRT1.1.\n"
] | Pacheco JM, Song L, Kuběnová L, Ovečka M, Berdion Gabarain V, Peralta JM, Lehuedé TU, Ibeas MA, Ricardi MM, Zhu S, Shen Y, Schepetilnikov M, Ryabova LA, Alvarez JM, Gutierrez RA, Grossmann G, Šamaj J, Yu F, Estevez JM. Cell surface receptor kinase FERONIA linked to nutrient sensor TORC signaling controls root hair growth at low temperature linked to low nitrate in Arabidopsis thaliana. New Phytol. 2023 Apr;238(1):169-185. doi: 10.1111/nph.18723. | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/nph.18723 | 2,023 | 30 | 0 | New Phytologist | true |
How the long non-coding RNA APOLO is able to control root hair growth under cold in Arabidopsis thaliana and which are the genes involved? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"The coding RNA APOLO do not bind the region responsible for the root hair (RH) repressor ROOT HAIR DEFECTIVE 6 (RHD6) and blocks the RHD6 kinase activity, resulting in cold-decresed RH elongation via the subsequent fosforilation of the transcription factor gene RHD6-like RSL4. Additionally, APOLO degrates the transcription factor WRKY42 and acts independetly of RHD6.",
"The long non-coding RNA APOLO identifies the region responsible for the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and modulates RHD6 transcriptional activity, resulting in cold-induced RH elongation via the subsequent activation of the transcription factor gene RHD6-like RSL4. Additionally, APOLO interacts with the transcription factor WRKY42 and regulates its association with the RHD6 promoter. ",
"The long non-coding RNA APOLO identifies the region responsible for the root hair (RH) repressor ROOT HAIR DEFECTIVE 6 (RHD6) and blocks the RHD6 transcriptional activity, resulting in cold-decresed RH elongation via the subsequent activation of the transcription factor gene RHD6-like RSL1. Additionally, APOLO do not interacts with the transcription factor WRKY42 and acts independetly of RHD6 promoter."
] | Moison M, Pacheco JM, Lucero L, Fonouni-Farde C, Rodríguez-Melo J, Mansilla N, Christ A, Bazin J, Benhamed M, Ibañez F, Crespi M, Estevez JM, Ariel F. The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold. Mol Plant. 2021 Jun 7;14(6):937-948. doi: 10.1016/j.molp.2021.03.008. | Model Organisms | GENE REGULATION | 10.1016/j.molp.2021.03.008 | 2,021 | 94 | 1 | Molecular Plant | true |
How auxin control ROS homeostasis and Root hair growth in Arabidopsis thaliana and which are the genes involved? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"ROS reduction in Arabidopsis thaliana is regulated by the transcription factor RSL4, which is transcriptionally repressed by auxin via several auxin response factors (ARFs). Auxin blocks ROS-mediated non-polar development of root hairs by repressing RSL4, which subsequently fosforilates the expression of genes encoding NADPH oxidases and class III peroxidases, responsible for degrading ROS molecules.",
"ROS generation is regulated by the transcription factor RSL4, which is transcriptionally modulated by auxin via several auxin response factors (ARFs) in Arabidopsis thaliana. Auxin regulates ROS-mediated polar development by activating RSL4, which subsequently enhances the expression of genes encoding NADPH oxidases and class III peroxidases, responsible for catalyzing ROS generation. ",
"ROS degration is regulated by the transcription factor RSL4, which is transcriptionally repressed by absisic acid via several auxin response factors (ARFs). Absisic acid triggers ROS-mediated isotropic development of lateral roots by repressing RSL4, which subsequently fosforilates the proteins encoding NADPH oxidases and class III peroxidases, responsible for nuclear ROS production."
] | Mangano S, Denita-Juarez SP, Choi HS, Marzol E, Hwang Y, Ranocha P, Velasquez SM, Borassi C, Barberini ML, Aptekmann AA, Muschietti JP, Nadra AD, Dunand C, Cho HT, Estevez JM. Molecular link between auxin and ROS-mediated polar growth. Proc Natl Acad Sci U S A. 2017 May 16;114(20):5289-5294. doi: 10.1073/pnas.1701536114. | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1073/pnas.1701536114 | 2,017 | 221 | 1 | Proceedings of the National Academy of Sciences | true |
How RALF1-FERONIA regulates specific mRNA translation in root hairs in Arabidopsis thaliana and which are the genes involved in this process? | GENE REGULATION - TRANSLATION | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the nuclear peptide RALF1 and its receptor, the FERONIA receptor kinase, blocks root hair tip development via regulating protein phosphorilation. RALF1 degradates FERONIA-mediated ubiquination of eIF4E1, a eukaryotic transcriptional initiation factor essential for regulating the mRNA transcription rate. Phosphorylated eIF4E1 enhances mRNA sintesis and regulates mRNA development, hence influencing gene expression. The mRNAs is degraded by the RALF1–FERONIA–eIF4E1 module include ROP2 and RSL4, which are minor regulators of root hair non polar proliferation.",
"In Arabidopsis thaliana, the cytoplasmic peptide RALF1 and its receptor, the FERONIA receptor kinase, repress root hair tip development via regulating protein degradation. RALF1 blocks the FERONIA-mediated phosphorylation of eIF4E1, a eukaryotic translation initiation factor essential for regulating the mRNA translation rate. Phosphorylated eIF4E1 decreases mRNA affinity and blocks mRNA translation, hence influencing protein synthesis. The mRNAs degraded by the RALF1–FERONIA–eIF4E1 module include ROP2 and RSL4, which are minor regulators of root hair cell polarity and proliferation.",
"In Arabidopsis thaliana, the extracellular peptide RALF1 and its receptor, the FERONIA receptor kinase, enhance root hair tip development via regulating protein synthesis. RALF1 enhances the FERONIA-mediated phosphorylation of eIF4E1, a eukaryotic translation initiation factor essential for regulating the mRNA translation rate. Phosphorylated eIF4E1 enhances mRNA affinity and regulates mRNA translation, hence influencing protein synthesis. The mRNAs affected by the RALF1–FERONIA–eIF4E1 module include ROP2 and RSL4, which are crucial regulators of root hair cell polarity and proliferation."
] | Zhu S, Estévez JM, Liao H, Zhu Y, Yang T, Li C, Wang Y, Li L, Liu X, Pacheco JM, Guo H, Yu F. The RALF1-FERONIA Complex Phosphorylates eIF4E1 to Promote Protein Synthesis and Polar Root Hair Growth. Mol Plant. 2020 May 4;13(5):698-716. doi: 10.1016/j.molp.2019.12.014. | Model Organisms | GENE REGULATION | 10.1016/j.molp.2019.12.014 | 2,020 | 112 | 2 | Molecular Plant | true |
Are plants and animals different in terms of the cellular compartments where r-proteins are encoded, and where are they encoded in each? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"Yes, they are different. Animal r-proteins are encoded exclusively by the nuclear genome. However, plant r-proteins can be encoded by the nuclear, mitochondrial, or plastid genomes, with some variation in the location of these genes across species.",
"Yes, they are different. Animal r-proteins are encoded by the nuclear and mitochondrial genomes, while plant r-proteins are encoded exclusively in the nucleus.",
"No, there are no differences. In both animals and plants, r-proteins are encoded by the nuclear and mitochondrial genomes. "
] | doi.org/10.1093/plcell/koac333 | Non-specific | GENE REGULATION | 10.1093/plcell/koac333 | 2,022 | 17 | 0 | The Plant Cell | true |
Which proteins are the molecular partners of the plant-specific non-canonical translation initiation protein CERES and what role does it play in translation? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"CERES is a plant-specific protein that interacts eIF4G isoforms and forms non-canonical initiation complexes that exclude eIF4A, eIF3 and PABP. In conditions where the metabolic and nutritional status of the plant is at its highest-level CERES complexes boost general translation and fine-tune the specific translation of a set of mRNAs involved in light response and saccharide management.",
"CERES is a plant-specific protein that interacts with the eIF4E isoforms and, in the absence of eIF4G isoforms, recruits eIF4A, eIF3 and PABP forming non-canonical initiation complexes. In conditions where the metabolic and nutritional status of the plant is at its highest-level CERES complexes boost general translation and fine-tune the specific translation of a set of mRNAs involved in light response and saccharide management.",
"CERES is a plant-specific protein that interacts with the eIF4E isoforms and, in the absence of eIF4G isoforms, recruits eIF4A, eIF3 and PABP forming non-canonical initiation complexes. CERES complexes are formed in conditions of plant stress and act down-regulating general translation as a means of energy conservation "
] | DOI: 10.1038/s41477-019-0553-2 | Non-specific | GENE REGULATION | 10.1038/s41477-019-0553-2 | 2,019 | 34 | 1 | Nature Plants | true |
How does EIN2 regulate the translation of EBF2 in response to the plant hormone ethylene? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"In the presence of ethylene, the C-terminal end of EIN2 is cleaved and released from the ER membrane. It translocates to the nucleus, where it participates in the transcriptional up-regulation of ethylene-responsive genes, including EBF2. In the cytoplasm, the EIN2 C-terminal end binds the 5' untranslated region (5' UTR) of EBF2 mRNA and impedes the binding of the cap-binding complex, inhibiting its translation. This mechanism explains the lack of EBF protein accumulation upon ethylene treatment despite high levels of EBF2 transcripts.",
"In the presence of ethylene, the C-terminal end of EIN2 is cleaved and released from the ER membrane. It translocates to the nucleus, where it participates in the transcriptional up-regulation of ethylene-responsive genes, including EBF2, and also to the cytoplasm. In the cytoplasm, the EIN2 C-terminal end binds the 3' untranslated region (3' UTR) of EBF2 mRNA and recruits the UPF proteins, the core components of the nonsense-mediated decay (NMD) machinery. This interaction leads to the sequestration of EBF2 mRNA into P-bodies, impeding its translation. This mechanism explains the lack of EBF protein accumulation upon ethylene treatment, despite high levels of EBF2 transcripts. ",
"In the presence of ethylene, the C-terminal end of EIN2 is cleaved and released from the ER membrane. It translocates to the nucleus, where it participates in the transcriptional up-regulation of ethylene-responsive genes, including EBF2, and also to the cytoplasm. In the cytoplasm, the EIN2 C-terminal end binds the 5' untranslated region (5' UTR) of EBF2 mRNA and recruits the downstream proteins of the ethylene signaling pathway. This interaction leads to the sequestration of EBF2 mRNA into P-bodies, impeding its translation. This mechanism explains the lack of EBF protein accumulation upon ethylene treatment, despite high levels of EBF2 transcripts."
] | doi.org/10.1016/j.cell.2015.09.036 | Non-specific | GENE REGULATION | 10.1016/j.cell.2015.09.036 | 2,015 | 269 | 1 | Cell | true |
Which proteins of the ethylene signaling pathway are required for the translational regulation of EBF2 in response to the plant hormone ethylene? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"The 3´UTR of EBF2 is the sole responsible for the translational regulation",
"EIN3 and EIL1",
"EIN2 and upstream components that guarantee perception of ethylene. "
] | doi.org/10.1016/j.cell.2015.09.036 | Non-specific | GENE REGULATION | 10.1016/j.cell.2015.09.036 | 2,015 | 269 | 2 | Cell | true |
Do upstream open reading frames (uORFs) regulate translation of the main ORF of their transcript? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"Yes. uORFs are short translated ORFs present in the 5′ leaders of mRNAs that usually repress translation of the main downstream ORF. The effectiveness of a uORF in repressing translation depends on several characteristics, such as the sequence context around its initiation codon, the length, the distance between its stop codon and the next ORF in the transcript, and/or the overlap of the uORF with the mORF ",
"No. uORFs are short translated ORFs present in the 5′ leaders of mRNAs that have no effect on the translation of the main downstream ORF. ",
"Yes. uORFs are short translated ORFs present in the 5′ leaders of mRNAs that usually enhance translation of the main downstream ORF. The effectiveness of a uORF in enhancing translation depends on several characteristics, such as the sequence context around its initiation codon, the length, the distance between its stop codon and the next ORF in the transcript, and/or the overlap of the uORF with the mORF"
] | doi.org/10.1111/tpj.13520 | Non-specific | GENE REGULATION | 10.1111/tpj.13520 | 2,017 | 163 | 0 | The Plant Journal | true |
Which proteins are part of the infectosome protein complex that directs the polar growth of rhizobia infection threads in legume root hairs? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"Vapyrin (VPY), RHIZOBIUM-DIRECTED POLAR GROWTH (RPG), E3 ligase LUMPY INFECTIONS (LIN), exocyst subunit EXO70H4.",
"Vapyrin (VPY), RHIZOID-DIRECTED POLAR GAMETE (RPG), E3 ligase LUMPY INFECTIONS (LIN), exocyst subunit EXO70H4.",
"Vapyryn (VPN), RHIZOBIUM-DIRECTED POLAR GROWTH (RDP), E3 ligase LUMPY INFECTIONS (LUN), exocyst subunit EXO70H4."
] | 10.1038/s41467-019-10029-y; 10.7554/eLife.80741; | Model Organisms | ENVIRONMENT | 10.7554/eLife.80741 | 2,023 | 23 | 0 | eLife | true |
The nitrogen-fixing nodule symbiosis is restricted to plant species belonging to four related angiosperm orders. Which are these four group of plants and which transcription factor, indispensable for root nodulation, has been fundamental in the evolution of this symbiosis? | ENVIRONMENT - PLANT-SYMBIONTS | [
"non-specific"
] | [
"The nitrogen-fixing nodule symbiosis occurs in plant species belonging to four related angiosperm orders, Fabales, Fagales, Crossosomatales, and Rosales, known as the nitrogen-fixing clade. The origin of this symbiosis can be traced back to a single ancestor, around 300 million years ago, and involved the recruitment of the transcription factor Nodule Inception (NIN), critical for nodulation in both legume and non-legume species. ",
"The nitrogen-fixing nodule symbiosis occurs in plant species belonging to four related angiosperm orders, Females, Fagales, Cucurbitales, and Rojales, known as the nitrogen-fixing clade. The origin of this symbiosis can be traced back to a single ancestor, around 100 million years ago, and involved the recruitment of the transcription factor Nodule Inceptor (NIN), critical for nodulation in both legume and non-legume species.",
"The nitrogen-fixing nodule symbiosis occurs in plant species belonging to four related angiosperm orders, Fabales, Fagales, Cucurbitales, and Rosales, known as the nitrogen-fixing clade. The origin of this symbiosis can be traced back to a single ancestor, around 110 million years ago, and involved the recruitment of the transcription factor Nodule Inception (NIN), critical for nodulation in both legume and non-legume species."
] | 10.1016/j.xplc.2019.100019; 10.1126/science.aat1743 | Non-specific | ENVIRONMENT | 10.1126/science.aat1743 | 2,018 | 333 | 2 | Science | true |
Cytoplasmic bridges are formed in plant cells to anticipate endosymbiotic infection by rhizobia-filled infection threads and arbuscular mycorrhizal fungal hyphae in Medicago. How are these cytoplasmic bridges called? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"PIT (Pre-Infection Thread) in the case of rhizobia infection and PPA (Pre-Penetration Apparatus) in the case of arbuscular mycorrhiza fungi infection.",
"PIT (Priming-Inside Thread) in the case of rhizobia infection and PPA (Pre-penetration Apparatus) in the case of arbuscular mycorrhiza fungi infection. ",
"PIT (Pre-Infection Thread) in the case of rhizobia infection and PPA (Pre-Priming Appendix) in the case of arbuscular mycorrhiza fungi infection. "
] | 10.1038/s41467-024-55067-3; 10.1146/annurev-cellbio-101512-122413 | Model Organisms | ENVIRONMENT | 10.1146/annurev-cellbio-101512-122413 | 2,013 | 442 | 0 | Annual Review of Cell and Developmental Biology | true |
The cell cycle status of plant cells is dynamically regulated during transcellular passage of rhizobial infection threads Medicago root cortex. What is the cell cycle status of plant cells during infection thread passage? Which symbiotic transcription factor is involved in regulating this process? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"Root cortical cells transcellularly crossed by an infection thread enter the cell cycle, but remain in a G2-post-replicative phase without mitosis. The transcription factor NF-YA1 was involved in the regulation of this process. ",
"Root cortical cells transcellularly crossed by an infection thread enter the cell cycle, but remain in a G1 cell cycle phase. The transcription factor NF-YA1 was involved in the regulation of this process. ",
"Root cortical cells transcellularly crossed by an infection thread enter the cell cycle, but remain in a G12-post-replicative phase without mitosis. The transcription factor NF-ABC was involved in the regulation of this process. "
] | 10.7554/eLife.88588.1 | Model Organisms | ENVIRONMENT | 10.7554/eLife.88588.1 | 2,023 | 0 | 0 | null | true |
Symplastic communication regulated by callose turnover at plasmodesmata is important for coordinating nodule development in Medicago. What is callose? and which enzyme was involved in degrading callose to promote symplastic connectivity during nodulation in Medicago? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"\nCallose is a β-1,3-chitin polysaccharide that, when deposited in plasmodesmata, reduces symplastic connectivity between cells. The Medicago β-1,3-glucoronidase MtGLU2, is a novel plasmodesmata-associated callose-degrading enzyme required for establishing symplastic connectivity during nodule development. ",
"Callose is a β-1,6-glucan polysaccharide that, when deposited in plasmodes, reduces symplastic connectivity between cells. The Medicago β-1,3-glucanase MtBG2 is a novel plasmode-associated callose-degrading enzyme required for closing symplastic connectivity during nodule development. ",
"Callose is a β-1,3-glucan polysaccharide that, when deposited in plasmodesmata, reduces symplastic connectivity between cells. The Medicago β-1,3-glucanase MtBG2 is a novel plasmodesmata-associated callose-degrading enzyme required for establishing symplastic connectivity during nodule development. "
] | 10.1016/j.cub.2018.09.031 | Model Organisms | ENVIRONMENT | 10.1016/j.cub.2018.09.031 | 2,018 | 53 | 2 | Current Biology | true |
In Arabidopsis thaliana, which transcription factors control DNA Damage Response genes in response to replication stress together with SOG1 ? Do they function cooperatively or antagonistically to control the expression of genes involved in cell cycle progression ? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis, E2FA and E2FB share many target genes with SOG1 and play a role in the plant’s response to replication stress. SOG1 activates its target genes, whereas E2FB can function both as a positive or a negative regulator of their shared targets. In particular, E2FB represses the expression of genes involved in cell cycle arrest, thereby allowing cell cycle progression in spite of replication stress.",
"In Arabidopsis, E2FA and E2FB do not share any target genes with SOG1 but play a role in the plant’s response to replication stress. SOG1 activates its target genes, whereas E2FA and E2FB function as negative regulators of their specific targets. In particular, E2FB represses the expression of genes involved in cell cycle arrest, whereas E2FA activates genes involved in cell cycle progression. Together, they allow cell cycle progression in spite of replication stress.",
"In Arabidopsis, E2FA shares many target genes with SOG1 and plays a role in the plant’s response to replication stress. Both SOG1 and E2FA function as a positive regulators of their shared targets. In particular, E2FA activates the expression of genes involved in cell cycle arrest, thereby playing a complementary role to that of SOG1 in promoting cell cycle arrest in response to replication stress."
] | https://doi.org/10.1016/j.molp.2023.07.002 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.molp.2023.07.002 | 2,023 | 7 | 0 | Molecular Plant | true |
How does the ATR-WEE1 module control SOG1 expression in response to replication stress in Arabidopsis thaliana, and what are the key proteins involved in this regulatory mechanism? | GENE REGULATION - TRANSLATION | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the ATR-WEE1 module represses SOG1 translation in response to DNA damage. In response to replication stress, WEE1 is transcriptionally activated by SOG1, and phosphorylated by ATR. WEE1 phosphorylates the GCN20 sub-unit of the GCN20-GCN1 dimer that activates translation, promoting GCN20 degradation, resulting in reduced SOG1 translation.",
"In Arabidopsis thaliana, the ATR-WEE1 module promotes SOG1 translation in response to DNA damage. In response to replication stress, WEE1 is transcriptionally activated by SOG1, and phosphorylated by ATR. WEE1 phosphorylates the GCN20 sub-unit of the GCN20-GCN1 dimer that represses translation, promoting GCN20 degradation, resulting in enhanced SOG1 translation.",
"In Arabidopsis thaliana, the ATR-WEE1 module represses SOG1 translation in response to DNA damage. In response to replication stress, WEE1 is transcriptionally activated by ATR, and phosphorylated by SOG1. SOG1 phosphorylates the GCN20 sub-unit of the GCN20-GCN1 dimer that represses translation, promoting GCN20 stabilization, resulting in reduced SOG1 translation."
] | https://doi.org/10.1093/plcell/koad126 | Model Organisms | GENE REGULATION | 10.1093/plcell/koad126 | 2,023 | 8 | 1 | The Plant Cell | true |
In Arabidopsis thaliana, how does TSK recognized newly replicated chromatin ? How does it mediate genomic instability in atxr5 atxr6 mutants? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis, TSK specifically interacts with the H3.1 histone variant that is incorporated into DNA during DNA replication through its TPR motif. Quickly after DNA replication, histone H3.1 is mono-methylated on lysin 27 by ATXR5 and ATXR6, which inhibits TSK binding, thereby restricting its activity to newly replicated DNA. In atxr5 atxr6 mutants, histone H3.1 is not methylated, which allows prolonged TSK binding and promotes homologous recombination at broken replication fork, thereby triggering heterochromatin amplification and genomic instability.",
"In Arabidopsis, TSK specifically interacts with the H3.1 histone variant that is incorporated into DNA during DNA replication through its TPR motif. Quickly after DNA replication, histone H3.1 is de-methylated on lysin 27 by ATXR5 and ATXR6, which promotes TSK binding, thereby restricting its activity to newly replicated DNA. In atxr5 atxr6 mutants, histone H3.1 is not de-methylated, which prevents TSK binding and prevents homologous recombination at broken replication fork, thereby triggering heterochromatin amplification and genomic instability.",
"In Arabidopsis, TSK specifically interacts with the H3.3 histone variant that is incorporated into DNA during DNA replication through its LPR motif. Quickly after DNA replication, histone H3.3 is mono-methylated on lysin 27 by ATXR5 and ATXR6, which inhibits TSK binding, thereby restricting its activity to newly replicated DNA. In atxr5 atxr6 mutants, histone H3.3 is not methylated, which allows prolonged TSK binding and promotes homologous recombination at broken replication fork, thereby triggering heterochromatin amplification and genomic instability."
] | doi:10.1126/science.abm5320 | Model Organisms | GENOME AND GENOMICS | 10.1126/science.abm5320 | 2,022 | 49 | 0 | Science | true |
How does SMR1 control leaf epidermis development at the cellular level in Arabidopsis thaliana, and how does it contribute to the plant’s response to environmental conditions? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis, SMR1 promotes the self-renewal of stomatal lineage ground cells and inhibits their differentiation into pavement cells by activating CYCA-CDKB1 complexes. In response to drought, down-regulation of SMR1 allows reducing the plant’s stomatal index, thereby leading to improved drought tolerance.",
"In Arabidopsis, SMR1 inhibits the self-renewal of stomatal lineage ground cells and promotes their differentiation into pavement cells by inhibiting CYCA-CDKB1 complexes. In response to drought, up-regulation of SMR1 allows reducing the plant’s stomatal index, thereby leading to improved drought tolerance.",
"In Arabidopsis, SMR1 inhibits the differentiation of stomatal lineage ground cells into pavement cells and promotes their proliferation by activating CYCA-CDKB1 complexes. Down-regulation of SMR1 reduces plant’s tolerance to drought while its over-expression improves plant’s tolerance to drought."
] | doi.org/10.1038/s41477-023-01452-7 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1038/s41477-023-01452-7 | 2,023 | 7 | 1 | Nature Plants | true |
Which kinase plays the most prominent role in Double-Strand Break repair in maize, and what is it's role during development? | CELL BIOLOGY AND CELL SIGNALING | [
"Zea mays"
] | [
"In Maize, ATR is the main kinase involved in the response to double-strand breaks whereas ATM plays only a minor role. During plant development, ATR is required for normal kernel development to prevent double-strand breaks accumulation and premature endoreduplication onset.",
"In Maize, both ATR and ATM play crucial roles in the response to double-strand breaks. During plant development, ATR is required for normal leaf development to prevent single-strand breaks accumulation and early senescence.",
"In Maize, ATM is the main kinase involved in the response to double-strand breaks whereas ATR plays only a minor role. During plant development, ATM is required for normal kernel development to prevent double-strand breaks accumulation and premature endoreduplication onset."
] | 10.1093/plcell/koab158 | Cereal Grains | CELL BIOLOGY AND CELL SIGNALING | 10.1093/plcell/koab158 | 2,021 | 28 | 0 | The Plant Cell | true |
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