Post‐translational modification of histones and DNA methylation are important components of chromatin‐level control of genome activity in eukaryotes. However, principles governing the combinatorial association of chromatin marks along the genome remain poorly understood. Here, we have generated epigenomic maps for eight histone modifications (H3K4me2 and 3, H3K27me1 and 2, H3K36me3, H3K56ac, H4K20me1 and H2Bub) in the model plant Arabidopsis and we have combined these maps with others, produced under identical conditions, for H3K9me2, H3K9me3, H3K27me3 and DNA methylation. Integrative analysis indicates that these 12 chromatin marks, which collectively cover ∼90% of the genome, are present at any given position in a very limited number of combinations. Moreover, we show that the distribution of the 12 marks along the genomic sequence defines four main chromatin states, which preferentially index active genes, repressed genes, silent repeat elements and intergenic regions. Given the compact nature of the Arabidopsis genome, these four indexing states typically translate into short chromatin domains interspersed with each other. This first combinatorial view of the Arabidopsis epigenome points to simple principles of organization as in metazoans and provides a framework for further studies of chromatin‐based regulatory mechanisms in plants.
Packaging of DNA into chromatin is pivotal for the regulation of genome activity in eukaryotes. The basic unit of chromatin is the nucleosome, which is composed of 147 bp of DNA wrapped around a protein octamer composed of two molecules each of the core histones H2A, H2B, H3 and H4. Covalent modifications of histones, DNA methylation, incorporation of histone variants, and other factors, such as chromatin‐remodelling enzymes or small RNAs, all contribute to defining distinct chromatin states that modulate access to DNA (Berger, 2007; Kouzarides, 2007). In particular, different histone modifications are thought to act sequentially or in combination in order to confer distinct transcriptional outcomes (Strahl and Allis, 2000; Jenuwein and Allis, 2001; Berger, 2007; Lee et al, 2010a). More generally, it is now well established that the precise composition of chromatin along the genome, which defines the epigenome, participates in the selective readout of the genomic sequence.
Thanks in part to a compact, almost fully sequenced and well‐annotated genome, the flowering plant Arabidopsis thaliana has become a model of choice for exploring the epigenomes of multicellular organisms and the contribution of chromatin to the regulation of genome activity during development or in response to the environment. Indeed, epigenomic profiling in Arabidopsis has begun to provide insights into the relationship between transcriptional activity and localization of chromatin marks or histone variants (Roudier et al, 2009; Feng and Jacobsen, 2011). For instance, H3K4me3 and H3K36me2 are detected at the 5′‐ and 3′‐ends of actively transcribed genes, respectively (Oh et al, 2008; Zhang et al, 2009), while H3K27me3 broadly marks repressed genes (Turck et al, 2007; Zhang et al, 2007; Oh et al, 2008). In contrast, cytosine methylation (5mC) has a dual localization. It is present predominantly over silent transposable elements (TEs) and other repeats, where it is associated with H3K9me2 and H3K27me1, but also in the body of ∼30% of genes, many of which are characterized by moderate expression levels (Lippman et al, 2004; Zhang et al, 2006; Zilberman et al, 2006; Turck et al, 2007; Vaughn et al, 2007; Bernatavichute et al, 2008; Cokus et al, 2008; Lister et al, 2008; Jacob et al, 2010). Furthermore, the variant histone H2A.Z, which is preferentially deposited near the 5′‐end of genes and promotes transcriptional competence, antagonizes DNA methylation and vice versa (Zilberman et al, 2008). However, extensive combinatorial analyses of these and other chromatin marks have not been performed so far in Arabidopsis and meta‐analysis of published data is complicated by the fact that biological materials and methodologies often differ between studies.
Here, we report the epigenomic profiles of eight histone modifications (H3K4me2, H3K4me3, H3K27me1, H3K27me2, H3K36me3, H3K56ac, H4K20me1 and H2Bub). Integrative analyses of these and other profiles, previously obtained under identical conditions for DNA methylation, H3K9me2, H3K9me3 and H3K27me3 (Turck et al, 2007; Vaughn et al, 2007), indicate a low combinatorial complexity of chromatin marks in Arabidopsis, as recently reported for metazoans (Wang et al, 2008; Hon et al, 2009; Ernst and Kellis, 2010; Gerstein et al, 2010; Roy et al, 2010; Kharchenko et al, 2011; Liu et al, 2011; Riddle et al, 2011; Zhou et al, 2011). Furthermore, our study identifies four main chromatin states in Arabidopsis, which have distinct indexing functions and which typically form short domains interspersed with each other. This first comprehensive view of the Arabidopsis epigenome suggests simple principles of organization, as recently proposed for Drosophila (Filion et al, 2010), and provides a resource to refine our understanding of the control of genome activity at the level of chromatin.
Epigenomic maps were generated for eight histone modifications (H3K4me2, H3K4me3, H3K27me1, H3K27me2, H3K36me3, H3K56ac, H2Bub and H4K20me1) using chromatin extracted from young seedlings and immunoprecipitation followed by hybridization to a tiling microarray that covers the entire chromosome 4 of Arabidopsis at ∼900 bp resolution (Turck et al, 2007). Data previously obtained for 5mC (Vaughn et al, 2007), H3K9me2, H3K9me3 and H3K27me3 (Turck et al, 2007) using similar materials and methodologies were also considered. Epigenomic profiling was additionally performed for seven of these marks (H3K4me2, H3K4me3, H3K27me1, H3K27me3, H3K36me3, H2Bub and 5mC) using a tiling microarray covering the whole‐genome sequence at 165 bp resolution. Chromosome 4 and whole‐genome maps were also obtained for histone H3 to control for nucleosome occupancy. The 12 marks were chosen because they were shown in previous studies to be associated with distinct transcriptional activities or subnuclear localization in Arabidopsis. In addition, our selection was focussed to a large extent on histone lysine methylation, which exists in three forms (mono‐, di‐ and tri‐methylation) and therefore has a versatile indexing potential (Sims and Reinberg, 2008).
Collectively, the 12 chromatin marks cover almost all of the regions that are detectably associated with histone H3, which amount to ∼90% of the total genome sequence (data not shown; Chodavarapu et al, 2010). The distribution of each chromatin modification was characterized in detail along chromosome 4. In agreement with previous reports (Lippman et al, 2004; Turck et al, 2007; Zhang et al, 2007, 2009; Oh et al, 2008; Tanurdzic et al, 2008), H3K4me2, H3K4me3, H3K9me3, H3K27me3 and H3K56ac are mostly found in euchromatin (Figure 1A; Supplementary Figure S1; Supplementary Table I), which reflects the fact that these different modifications are associated almost exclusively with genes (Figure 1B). H2Bub and H3K36me3, for which no epigenomic maps have been reported to date in plants, are also characterized by a predominant distribution over genes. In contrast, H4K20me1 is found in heterochromatin mainly and associates with TE and other repeat element sequences (Figure 1B), like H3K9me2 (Lippman et al, 2004; Bernatavichute et al, 2008). The present analysis reveals in addition that, like 5mC (Zhang et al, 2006; Zilberman et al, 2006), H3K27me1 and H3K27me2 are dual marks associated not only with TEs but also with a fraction of genes (Supplementary Tables II–IV).
Genomic distribution of chromatin marks. (A) Relative coverage of chromatin marks in the euchromatin and heterochromatin of chromosome 4. Coordinates for heterochromatin are 1.61–2.36 Mb (knob) and 2.78–5.15 Mb (pericentromeric regions). (B) Chromosome‐wide distribution of chromatin marks over annotated features. Tiles that overlap annotated genes or transposable elements (TAIR8) by at least 50 bp were assigned to the corresponding annotation and otherwise called 'intergenic'. (C) Pairwise association analysis of the 12 chromatin marks along chromosome 4. Mean association values were calculated for each pair of modifications over all marked tiles and are shown as a directional heat map organized by hierarchical clustering using Pearson's correlation distances.
Each chromatin mark defines domains of contiguous tiles and the number of these domains ranges from 306 for H3K9me2 to 1163 for H3K4me3. For H3K4me3, H3K36me3, H3K56ac, H3K9me3, H2Bub or H3K27me3, domains have similar median length between euchromatin and heterochromatin and mostly coincide with single transcription units (Supplementary Table II; Supplementary Figure S2). By contrast, H3K9me2, H4K20me1, H3K27me1, H3K27me2 and 5mC form small domains in euchromatin but large domains in heterochromatin, as a result of the dense clustering of TE and other repeat sequences in the latter (Supplementary Figure S2; Supplementary Table II).
As a first step in exploring the combinatorial deposition patterns of chromatin marks, unbiased pairwise association analyses were carried out. A heat map generated from the calculated association values (Supplementary Table V) and organized by hierarchical clustering reveals two clear groups of correlated pairs that distinguish genes from TE sequences (Figure 1C). Next, co‐occurrence of marks was registered over each of the ∼20 000 tiles of the chromosome 4 array. Of the 212=4096 combinations theoretically possible, only 665 were observed and among these, only 38 concerned at least 100 tiles (Supplementary Figure S3A). This indicates therefore a limited repertoire of chromatin signatures in Arabidopsis, as in other eukaryotes (Ernst and Kellis, 2010; Kharchenko et al, 2011; Liu et al, 2011). The four prevalent combinations of marks are H3K27me1+5mC+H3K9me2+H4K20me1+H3K27me2, H3K56Ac+H2Bub+H3K4me3+H3K4me2+H3K9me3+H3K36me3, H3K27me3+H3K27me2+H3K4me2 and H3K27me3+H3K27me2, which cover 10.9, 6.8, 4.7 and 4.6% of the tiling array, respectively. Whereas the first combination is almost exclusively associated with TE sequences, the other three are mainly present over genes (Supplementary Figure S3B). Furthermore, like H3K27me3+H3K27me2, most of the remaining combinations represented by at least 100 tiles are subcombinations of the three prevalent ones (Supplementary Figure S3B and data not shown).
To complement this tile‐centric analysis and to identify the prevalent combinatorial patterns of the 12 chromatin marks, unsupervised c‐means clustering was performed. The number of clusters (k) was varied from 2 to 11 and k=4 was determined to be optimal in maximizing homogeneity within clusters and heterogeneity between them. The four chromatin states (CS1–CS4) defined by these four clusters are also identified by PCA analysis (data not shown), thus reinforcing their significance. Whereas CS1 regroups ∼90% of the tiles associated with H3K4me3, H3K36me3, H3K9me3 and H2Bub as well as the majority of H3K4me2‐ and H3K56ac‐marked sequences, H3K27me3 and H3K27me2 are the most prevalent modifications in CS2 (Figure 2A). As expected from their composition, CS1 and CS2 are mainly associated with genes (Figure 2B) and have antagonistic indexing functions, being prevalent among active and repressed/lowly expressed genes, respectively (Figure 2C). CS3, which is associated predominantly with TE sequences (Figure 2B), regroups most of the tiles marked by H3K9me2, H4K20me1 and H3K27me1 as well as ∼50% of those marked by H3K27me2 and 5mC (Figure 2A). In contrast to the other three chromatin states, CS4 is not particularly enriched in any chromatin mark (Figure 2A) and is found mainly outside of genes and TE sequences (Figure 2B). Nonetheless, CS4 also marks ∼10% of genes, most of which display low expression (Figure 2C). In keeping with the domain layout of individual marks, CS1–CS4 typically form small domains interspersed with each other, except in cytologically defined heterochromatin, where CS3 forms larger domains as a result of the clustering of TE sequences (Figure 2D; Supplementary Figure S4).
The Arabidopsis epigenome contains four predominant chromatin states. (A) The table on the left indicates the composition of the four predominant chromatin states (CS) identified by c‐means clustering. The distribution of the 12 chromatin marks over the four CS is indicated as a heat map for values ranging from 25% (light purple) to 100% (dark purple). The degree of homogeneity of each CS is indicated by the percentage of tiles assigned to it that are associated with each of the 12 chromatin marks (numbers inside cells). Note that no single mark is present over >20% of the tiles assigned to CS4, in contrast to what is observed for CS1–CS3. The percentage of genes indexed by CS1, CS2 and CS4 and the percentage of TE annotations indexed by CS3 are also shown. Pie charts indicate the relative genomic coverage of the four CS and the number of domains that they each form. Grey colour corresponds to tiles that cannot be unambiguously assigned to any of the four CS (see Materials and methods). (B) Relative proportion of genomic features within each CS. Tiles that overlap annotated genes or transposable elements (TAIR8) by at least 50 bp were assigned the corresponding annotation. All other tiles were considered as 'intergenic'. (C) Relationship between chromatin states and gene expression level. The percentage of tiles associated with a given CS is represented according to expression level. The dashed line represents the distribution of all annotated genes of chromosome 4. Expression data (Schmid et al, 2005) were obtained by averaging appropriate developmental stages. (D) Distribution of the four CS along chromosome 4. For each tile, membership to a given CS is colour coded. K: heterochromatic knob. The non‐sequenced part of the centromere (C) is represented by the vertical black line. The high interspersion of chromatin states seen outside of heterochromatin is highlighted in a genome browser view of a 30‐kb euchromatic region (positions 0.95–0.98 Mb).
To investigate further the chromatin indexing of genes, pairwise analysis of chromatin modifications was carried out specifically over genic tiles, which revealed a tight association between H3K4me3 and H3K56ac, between H3K36me3, H3K9me3 and H2Bub and between H3K27me2 and H3K27me3 (Figure 3A). Next, average enrichment levels were calculated within and around genes for all marks except H3K9me2 and H4K20me1, which are almost exclusively associated with TE and other repeat sequences. As shown in Figure 3B, values are highest within the transcribed region for the 10 chromatin modifications considered and are typically lowest upstream or downstream of it. However, distribution patterns vary substantially between marks, as previously established in several instances (Turck et al, 2007; Zhang et al, 2007; Jacob et al, 2010). H3K4me3, H3K56ac, H3K4me2, H3K36me3 and H3K9me3 all peak at the 5′‐end of the transcribed region, but the first two marks more sharply than the other three (Figure 3B). In contrast, H2Bub as well as H3K27me1 are highest more centrally, 5mC is most enriched in the 3′‐half of the transcribed region and both H3K27me2 and H2K27me3 show an even distribution across transcribed regions. Finally, H3K27me2 differs from all other marks including H3K27me3 in that it remains high in flanking regions, a difference which does not result from the presence of H3K27me2‐marked TE sequences adjacent to genes nor from the lower signal to noise ratio measured for this mark (see legend of Figure 3A, data not shown). Using the genome‐wide profiles obtained for seven chromatin modifications, we could show in addition that contrary to H3K27me3, which preferentially marks small genes as noted before (Luo and Lam, 2010), H2Bub, H3K36me3, 5mC and, to a lesser extent, H3K4me2 as well as H3K4me3 tend to be associated with longer genes (Figure 3C). Unlike these chromatin modifications, H3K27me1 does not exhibit preferential association in relation to gene length (Figure 3C).
Distribution of chromatin marks over genes. (A) Pairwise association analysis of the 12 chromatin marks along chromosome 4. Mean association values were calculated for each pair of modifications over all marked genic tiles and are shown as a directional heat map organized by hierarchical clustering using Pearson's correlation distances metric. (B) Mean enrichment levels relative to histone H3 are plotted along marked genes (transcribed region, scaled to accommodate for different gene lengths, bin size of 1%) as well as up to 1 kb of upstream and downstream sequences (bin size of 10 bp). Maximum value for any given mark is arbitrarily set to 1. Data were obtained using the chromosome 4 tiling array. Note that values for H3K27me2 in upstream and downstream regions are significantly higher than for unmarked genes (>0.9 versus ∼0.6, not shown). (C) Left panels: Enrichment levels relative to histone H3 for marked genes sorted by length. Each line represents a single gene as well as 1 kb of upstream and downstream sequences. Enrichment is indicated as a heat map, with maximal (red) and minimal (green) values set to 1 and 0, respectively. Right panels: Frequency distribution of marked (red line) and all genes (black dashed line) according to their length. Data were obtained using the whole‐genome tiling array.
It has been established that H3K4me3 and H3K56ac mark genes that are highly and broadly expressed (Oh et al, 2008; Tanurdzic et al, 2008; Zhang et al, 2009). Conversely, H3K27me3 is preferentially associated with genes that are expressed at low levels or in a tissue‐specific manner (Turck et al, 2007; Zhang et al, 2007; Oh et al, 2008; Jacob et al, 2010) and 5mC tends to mark moderately expressed genes (Zilberman et al, 2006; Vaughn et al, 2007). Our analysis confirms these results and indicates in addition that H2Bub, H3K36me3 and H3K9me3 tend to mark highly expressed genes, like H3K4me3 and H3K56ac (Figure 4A). On the other hand, H3K4me2 does not appear to index genes in relation to their expression level and H3K27me1 as well as H3K27me2 tend to be associated with genes that are expressed at low level or in a tissue‐specific manner, like H3K27me3 (Figure 4A and B). However, H3K27me1 and H3K27me2/3 mark largely non‐overlapping sets of genes with different ontologies (Figure 3A; Supplementary Tables III, IV, VI and VII), which suggests the existence of two distinct gene repression systems associated with methylation of H3K27. For most chromatin marks, average enrichment levels correlate either positively or negatively with expression levels (Figure 4C). Thus, values for H3K4me3, H3K56ac, H3K36me3, H2Bub and H3K9me3 increase gradually with gene expression, at least up to mid expression levels, whereas values for H3K27me1, H3K27me2 and H3K27me3 show an opposite trend. Whether these correlations reflect expression of genes in a variable number of cells, or true differential enrichment in relation to expression level, remains to be determined.
Chromatin indexing in relation to gene expression. (A) Distribution density of marked genes according to expression percentiles. Genes were binned according to their absolute expression values in whole seedlings. The dashed line indicates the distribution of all annotated genes on chromosome 4 across all expression percentiles. Expression data (Schmid et al, 2005) were obtained by averaging appropriate developmental stages. (B) Tissue specificity of marked genes as estimated by Shannon entropy calculation. Low entropy values indicate high tissue specificity. The fraction of marked genes associated with a given entropy value is plotted for each chromatin modification. (C) Relationship between gene expression and enrichment level for each chromatin modification. Maximum enrichment level is set to 1 in each case.
Collectively, our findings indicate that H3K4me3 and H3K27me3 are diagnostic of two antagonist chromatin states that are associated with most active and repressed genes, respectively. However, ∼13% (3433 out of 27 294) of genes marked by H3K4me3 or H3K27me3 in whole seedlings present both marks, in agreement with previous observations (Oh et al, 2008; Zhang et al, 2009). To explore this further, H3K4me3 and H3K27me3 were mapped genome‐wide using chromatin extracted from roots and profiles were compared with those obtained for whole seedlings (this study) or aerial parts only (Oh et al, 2008). Out of the 3433 genes with both marks in whole seedlings, 284 genes (8.3%) are only marked by H3K4me3 in roots and by H3K27me3 in aerial parts or vice versa (Figure 5A; Supplementary Table VIII). Correspondingly, a majority of these genes show differential expression between roots and aerial parts (Figure 5B), which is in contrast to genes with persistent co‐marking in both plant parts (Figure 5A and C). Thus, it can be concluded that co‐marking in whole seedlings results for a number of genes from the mixing of cells with opposite chromatin indexing in the two plant parts. By extension, it is likely that persistent co‐marking in one or the other plant parts (Figure 5A) reflects similar mixing of cells with distinct epigenomes, but this time within organs. Co‐marking could nevertheless correspond to bona fide bivalent marking in some cases, as originally reported in mammals for key regulatory genes poised for activation (Wang et al, 2009) and as also described in Arabidopsis for a small number of genes encoding transcription factors (Jiang et al, 2008; Berr et al, 2010). In this respect, it is noteworthy that ontology analysis of the 224 genes with persistent co‐marking in both roots and aerial parts (Figure 5A) indicates significant enrichment for terms associated with regulation of transcription (data not shown).
Analysis of genes co‐marked with H3K27me3 and H3K4me3 in whole seedlings. (A) The 3433 genes co‐marked in whole seedlings were split into different classes according to their marking in roots (R; this study) and aerial parts (AP; Oh et al, 2008). 'Others' indicate genes with other marking patterns in the two plant parts. This class, which is not expected based on the co‐marking observed in whole seedlings, can be explained in part by the fact that the different data sets were not all generated using the same conditions and methodologies. (B) Expression analysis in roots and shoots (Schmid et al, 2005) for the 284 genes showing opposite marking in roots and aerial parts. Brown dots indicate genes with H3K4me3 in roots and H3K27me3 in aerial parts, green dots indicate genes with the opposite marking pattern. (C) Expression analysis in roots and shoots (Schmid et al, 2005) for the 224 genes showing persistent co‐marking in roots and aerial parts.
Using an integrative analysis of the distribution of 12 chromatin marks, we show that the Arabidopsis epigenome is organized around four predominant chromatin states with distinct biochemical, transcriptional and sequence properties. This representation refines the classical segmentation between cytologically defined heterochromatin and euchromatin. A first chromatin state (CS1) corresponds to transcriptionally active genes and is typically enriched in the trimethylated forms of H3K4 and H3K36. Two further states correspond to two distinct types of repressive chromatin. H3K27me3‐marked repressive chromatin (CS2) is mainly associated with genes under PRC2‐mediated repression (Turck et al, 2007; Zhang et al, 2007), while H3K9me2‐ and H4K20me1‐marked repressive chromatin (CS3) corresponds to classical heterochromatin and is almost exclusively located over silent TEs (Lippman et al, 2004; Bernatavichute et al, 2008). A fourth chromatin state (CS4) is characterized by the absence of any prevalent mark and is associated with weakly expressed genes and intergenic regions.
This rather simple organization of Arabidopsis chromatin into four main states shows similarities with that recently reported for Drosophila cells. Indeed, based on the integration of epigenomic maps obtained for 53 chromatin proteins, it was concluded that the Drosophila epigenome is organized into a mosaic of five principal chromatin types that display distinct functional properties (Filion et al, 2010). Specifically, Arabidopsis CS2 and CS3 are similar to Drosophila 'BLUE' and 'GREEN' chromatin types, which correspond to repressive chromatin associated with the Polycomb pathway and classical heterochromatin, respectively. Furthermore, CS4, which has no prevalent chromatin mark and indexes some weakly expressed genes as well as intergenic regions is reminiscent of Drosophila 'BLACK' chromatin, which is relatively gene poor and constitutes a repressive environment distinct from heterochromatin. In contrast, transcriptionally active chromatin is represented by a single chromatin state in Arabidopsis (CS1) but by two distinct types in Drosophila that differ in several ways, including the enrichment of H3K36me3 in 'YELLOW' but not in 'RED' chromatin.
Other large‐scale epigenomic studies have been performed in yeast (Liu et al, 2005), C. elegans (Gerstein et al, 2010; Liu et al, 2011), Drosophila (Kharchenko et al, 2011; Roy et al, 2010; Riddle et al, 2011) and human cells (Wang et al, 2008; Hon et al, 2009; Ernst and Kellis, 2010; Zhou et al, 2011), which all indicate a relatively low combinatorial complexity of chromatin marks. Furthermore, the two main repressive chromatin states defined in Arabidopsis (CS2 and CS3) have similar counterparts in metazoans, indicating that they are highly conserved between plants and animals. On the other hand, the single predominant chromatin state (CS1) that we have identified for transcriptionally active genes in Arabidopsis has no obvious equivalent in these other organisms. Instead, several chromatin states have been associated with expressed genes in other organisms. This discrepancy likely results from the smaller size of genes and intergenic regions in Arabidopsis (∼2 kb each on average), as well as the relatively lower resolution of our data. Indeed, our analysis shows that distribution patterns vary substantially between chromatin marks associated with active genes (Figure 3B), which suggests that CS1 could be further refined into at least two additional chromatin signatures, specific to the promoter and transcribed region of these genes.
Although the number of chromatin states identified via this type of integrative approach may appear surprisingly low, such analyses aim to identify prevalent combinations of chromatin marks or chromatin proteins. Furthermore, the heterogeneity of the biological material used in many of these studies, including ours, likely hampered the detection of certain chromatin states such as those that are specific to rare cell types. Ultimately, only a knowledge of the epigenomes of individual cell types will enable a full understanding of the functional impact of chromatin‐level regulation on genome activity.
Our work indicates that the Arabidopsis epigenome is mainly organized at the level of single transcription units and that the distribution of chromatin marks along genes is linked to the transcription process (Figures 2 and 3). For example, H3K4me3 peaks around the transcription start site of actively expressed genes, as observed in all other eukaryotes examined to date (Rando and Chang, 2009). Similarly, H3K56ac is specifically located at gene promoters and shows preferential marking of active genes, suggesting that, like in yeast, it could facilitate rapid transcriptional activation (Williams et al, 2008). In contrast to H3K4me3, H3K4me2 shows no particular association with highly expressed genes or with specific parts of genes. Rather than being a constitutive mark of transcription, H3K4me2 may be implicated in fine tuning of tissue‐specific expression, as recently reported in mammals (Pekowska et al, 2010).
The distribution of H3K36me3, H3K9me3 and H2Bub over the transcribed regions of expressed genes suggests that these modifications are linked with transcriptional elongation. In the case of H2Bub, this is in agreement with the distribution reported in mammals and yeast (Minsky et al, 2008; Schulze et al, 2009). For H3K9me3, enrichment over the coding region of expressed genes in Arabidopsis (this study; Caro et al, 2007; Turck et al, 2007; Charron et al, 2009) contrasts with the enrichment predominantly over heterochromatin in animals. However, association with the transcribed regions of some active genes has been reported in mammals (Vakoc et al, 2005, 2006; Squazzo et al, 2006). Whether H3K9me3 could serve different outcomes depending on genomic and or chromatin context and whether it has any role in transcription regulation in plants remains to be determined. Given the discrepancy between the low amounts of H3K9me3 reported in bulk histones (Jackson et al, 2004; Johnson et al, 2004) and its apparent abundance reported by ChIP‐chip, it is also possible that the H3K9me3 antibody we used recognizes another modification in Arabidopsis, which would be H3K36me3 based on our epigenomic analysis. However, in vitro competition assays using an H3K36me3 peptide suggest that this is unlikely (Supplementary Figure S5).
H3K36me3 preferentially marks exons of transcribed genes in yeast, C. elegans and mammals (Kolasinska‐Zwierz et al, 2009) and it was shown to be involved in the control of alternative splicing in mammals (Luco et al, 2010). In Arabidopsis, however, H3K36me3 peaks in the first half of the coding region, which is in contrast to the 3′‐end enrichment reported in other organisms (Wang et al, 2009). This preferential enrichment at the 5′‐end, which is not dependent on gene length, could indicate that the principles governing H3K36me3 deposition differ between plants and other eukaryotes. In fact, H3K36me3 distribution in Arabidopsis resembles that of H3K79me3 in mammals (Wang et al, 2009). As Arabidopsis lacks a clear homologue of the H3K79 methyltransferase Dot1 and has no H3K79me3 (Zhang et al, 2007), it is possible that H3K36me3 in plants serves a function equivalent to H3K79me3 in other eukaryotes. Furthermore, H3K36me2 could have a role similar to that attributed to H3K36me3 in other eukaryotes, as it peaks at the 3′‐end of expressed genes in Arabidopsis (Oh et al, 2008).
Chromatin marks associated with transcription have been proposed to cross talk and serve as checkpoints in budding yeast and mammals (Suganuma and Workman, 2008; Weake and Workman, 2008; Lee et al, 2010a). A similar scenario could be envisioned in Arabidopsis based on the chromatin marks that predominate in CS1, whereby the RNA polymerase II‐associated factor 1 complex would induce mono‐ubiquitylation of H2B via the activity of the Rad6‐Bre1 ubiquitin ligase homologues UBC1, 2 and 3 as well as HUB1 and 2, as shown at the FLC gene (Cao et al, 2008; Gu et al, 2009; Schmitz et al, 2009). H2Bub deposition would in turn help recruit COMPASS (COMplex Proteins ASsociated with Set1), thus mediating deposition of H3K4me3 and potentially H3K36me3 (in place of H3K79me3) as well as H3K36me2. Similarly to other eukaryotes, initiation of another round of transcription would require the activity of the Ubp8 ubiquitin protease homologue, UBP26, which catalyses H2B deubiquitylation (Sridhar et al, 2007). Consistent with this, H3K36me3 but not H3K36me2 nor H3K4me3 is almost lost at the 5′‐end of the gene FLC in ubp26 mutant plants and this loss is associated with a reduction of FLC expression (Schmitz et al, 2009). The steady‐state distribution pattern of H2Bub observed over expressed genes presumably results from targeted deubiquitylation of H2B at the 5′‐end and probably 3′‐end of the transcribed region, rather than from an increased ubiquitylation of H2B towards the middle of the gene.
Our epigenomic profiling of the three forms of H3K27 indicates that methylation of this lysine residue is generally associated with repressive chromatin and that its indexing function depends on the degree of modification (mono‐, di‐ and tri‐methylation). Thus, in agreement with previous studies, H3K27me3, which is the hallmark of CS2, is almost exclusively present over transcriptionally repressed genes (Turck et al, 2007; Zhang et al, 2007), while H3K27me1 is prevalent over silent TEs in pericentromeric regions, where it is thought to prevent over‐replication (Jacob et al, 2009, 2010). Our analysis reveals in addition that H3K27me2 is enriched over H3K27me3‐marked genes, as well as of over TE sequences. Although immunolocalization of H3K27me2 at chromocenters (Fuchs et al, 2006) was proposed to result from cross‐reactivity of antibodies with H3K27me1 in Arabidopsis (Jacob et al, 2009), we did not observe extensive cross‐reactivity of the H3K27me2 antibodies used in our study with H3K27me1 (Supplementary Figure S5). Moreover, while all forms of methylated H3K27 can be found over genes and are associated with transcriptional repression, little overlap is observed between the small group of genes marked by H3K27me1 and the much larger set of genes marked by H3K27me2/3, suggesting that these modifications define two repressive pathways with distinct gene targets (Supplementary Tables VI and VII). Whereas H3K27me3 deposition is catalysed by the evolutionarily conserved Polycomb Repressive Complexes 2 (Kohler and Hennig, 2010; Bouyer et al, 2011), H3K27me1 deposition over TE sequences is partly dependent on the activity of the two SET‐domain proteins ATXR5 and ATXR6 (Jacob et al, 2009). Whether H3K27me1 deposition over genes requires the same or different histone methyltransferases and whether it is associated with the control of DNA replication remain to be determined. Irrespective of the mechanisms involved, it is noteworthy that whereas H3K27me1‐marked TE sequences are also co‐marked with H3K9me2 and 5mC, this is not the case for H3K27me1‐marked genes.
Acetylation of H3K56 is another chromatin mark that has been linked with the replication process. In Arabidopsis cell cultures, early replicating sequences form broad domains of H3K56ac (Lee et al, 2010b). Our epigenomic profiling of H3K56ac reveals mostly short domains located at the 5′‐end of expressed genes, which correspond to the replication‐independent incorporation of acetylated H3K56. However, a few large domains (∼20 kb) are also detected, which span several genes, intergenic regions and TEs. As our epigenomic maps have been derived from whole seedlings that comprise only a small proportion of mitotic cells, these large H3K56ac domains might correspond to sequences frequently used as endoreplication origins.
Although most Arabidopsis genes are associated with chromatin states CS1 or CS2, ∼10% are instead associated with CS4, which is characterized by the absence of any prevalent chromatin mark among the 12 that were analysed in this work (Figure 3). Analysis of additional chromatin marks and proteins will be required to determine more precisely the nature of CS4 and notably the extent of its similarity to the repressive chromatin type BLACK of Drosophila (Filion et al, 2010).
To conclude, the first integrative view of the Arabidopsis epigenome provided here could be compared with a first sketch, which is progressively refined until a complete blueprint is produced. Importantly, key aspects of the Arabidopsis epigenome are already apparent in this first sketch, like the relative simplicity of designing principles, which appears to be shared with metazoans.
All experiments were performed using wild‐type Arabidopsis thaliana accession Columbia seedlings grown for 10 days either in liquid MS (whole seedlings) or on MS agar plates (roots and aerial parts) supplemented with 1% sucrose under long day conditions. ChIP and Me‐DIP assays were carried out essentially as described (Lippman et al, 2005) using commercially available antibodies (Supplementary Table IX; Supplementary Figure S5). Specificity of the H3K27me2 and H3K9me3 antibodies was tested by peptide competition and western blotting analysis on nuclear extracts (Supplementary Figure S5) as described in Bouyer et al (2011) using H3K27me3, H3K27me2, H3K27me1, H3K9me3 and H3K36me3 peptides (Millipore, 12‐565, 12‐566, 12‐567, 12‐568 and Diagenode sp‐058‐050, respectively). Immunoprecipitated DNA (IP) and input DNA (INPUT) were amplified, differentially labelled and co‐hybridized in dye‐swap experiments as described (Lippman et al, 2004; Turck et al, 2007) for the chromosome 4 tiling array or according to the manufacturer's instructions for the Roche NimbleGen whole‐genome tiling array. Two biological replicates were analySed (two dye‐swaps). The chromosome 4 array contains 21 800 printed features, on average ∼900 bp in size. The heterochromatic knob on the short arm and several megabases of pericentromeric heterochromatin are included and account for 16% of the 18.6 Mb covered by the array. Details of array design and production are described in Vaughn et al (2007). This platform has been deposited to GEO under accession number GPL10172. The whole‐genome tiling array consists of 50–75 nt tiles, with 110 nt spacing on average, that are tiled across the entire genome sequence (TAIR7), without repeat masking. Tiles have a melting temperature of 74°C on average and 88% of them match a unique position in the genome. This custom design was either split into two arrays of 360 718 tiles each, with every other tile on each array (GEO accessions GPL10911 and GPL10918) or synthesized in triplicates of 711 320 tiles each on a single array (GEO accession GPL11005).
Hybridization data were normalized as described previously for the chromosome 4 array (Turck et al, 2007) or using an ANOVA model was applied to remove technical biases from data obtained using the whole‐genome array. Data were averaged on the dye‐swap to remove tile‐specific dye bias. Normalized data were analysed using the ChIPmix method (Martin‐Magniette et al, 2008), which was adapted to handle multiple biological replicates simultaneously. This method is based on a mixture model of regressions, the parameters of which are estimated using the EM algorithm. For each tile, a posterior probability is defined as the probability to be enriched given the log(Input) and log(IP) intensities, and is used to assign each tile into a normal or enriched class. A false‐positive risk is determined by defining the probability of obtaining a posterior probability at least as extreme as the one that is actually observed when the tile is normal. False‐positive risks are then adjusted by the Benjamini–Hochberg procedure and tiles for which the adjusted false‐positive risk is <0.01 are declared enriched. Previously published data (Turck et al, 2007; Vaughn et al, 2007) were re‐analysed using the same procedure. Neighbouring enriched tiles are joined into domains by requiring a minimal run of 1.6 kb or 400 bp and allowing a maximal gap of 800 or 200 bp for data obtained using the chromosome 4 or whole‐genome arrays, respectively. Thus, 'singletons' are not considered for further analyses.
General bioinformatics methods including positional, quantitative and class‐based computations were conducted in Excel and using ad hoc scripts written in R, PERL or Python. Genes and transposable elements were annotated based on TAIR8 and other sequences are assumed to be intergenic. Gene Ontology analyses were done using the GOrilla (Eden et al, 2009) with an additional correction for multiple testing of the P‐values. Pairwise association analysis, which is directional unlike correlation analysis, was calculated by scoring the frequency of co‐occurrence of pairs of chromatin modifications among the 12 marks analysed on the chromosome 4 tiling array.
Whole seedlings transcriptome data were retrieved from Schmid et al (2005) and genes were binned into 20 expression percentiles according to their absolute expression values. Within each expression percentile, the number of genes marked by a given chromatin modification was calculated and represented as a percentage of all the genes marked by this modification. Shannon entropy for each set of marked genes was calculated as described (Zhang et al, 2006) using publicly available developmental expression series (Schmid et al, 2005), after filtering genes that showed no expression in any conditions.
Fuzzy c‐means clustering using R MCLUST package was performed to classify tiles into principal chromatin states based on the 12 epigenomic maps. c‐means clustering computes membership values for each tile towards all the clusters and all the membership values add up to 1. Each tile was assigned to one cluster only, based on a membership value equal or higher to 0.5. To identify the optimal number of clusters (k), cluster validity value, which is an estimate of homogeneity within the clusters and heterogeneity between them, was calculated for clusters from k=2–11.
Raw and processed data have been deposited to NCBI's Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) under the super‐series accession GSE24710 and to CATdb (http://urgv.evry.inra.fr/CATdb) (Samson et al, 2004; Gagnot et al, 2008). In addition, array data and genome annotation are displayed using a Generic Genome Browser, available for visualization at http://epigara.biologie.ens.fr/index.html.
We thank members of the Colot group and Edith Heard for critical reading of the manuscript. This work was supported by grants from the Agence Nationale de la Recherche (ANR Genoplante TAG and REGENEOME, ANR blanc DDB1, ANR Sysbio) and by the European Union Network of Excellence 'The Epigenome'. IA, AS and SC were supported by PhD studentships from the ANR, the Centre National de la Recherche Scientifique (CNRS) and the Ministère de l'Enseignement Supérieur et de la Recherche (MESR), respectively.
Author contributions: FR and VC conceived and designed the experiments. FR, SC, DB, EC, LG, BD, SDr and FB performed the experiments. FR, IA, AS and VC analysed the data. CBe, TM‐H, ED‐B, LA‐S, SDe, VB, SA, AS, CBo, M‐LMM, SR and MC contributed reagents/materials/analysis tools. FR and VC wrote the paper.


text:
Our Responsibility to Stand Against Christian Nationalism: Executive Council Opening Remarks
President Jennings gave these opening remarks to an online meeting of Executive Council on January 22:
Hello, and welcome to this online meeting of Executive Council. We're beginning to get good at meeting this way!
I'm grateful for this technology that allows our work to continue, but just because it has become routine, I don't want to minimize the strain that it places on many of us and the staff who support our work. Thank you for your continuing perseverance in the face of Zoom fatigue, barking dogs, children home from school, glitchy home wifi, and the endless challenges of the mute button, not to mention economic uncertainty, spiraling COVID infection rates, and an existential crisis in the democracy of the United States. We see you, and we are grateful.
I want to spend my time today reflecting with you on what I believe our church is called to do about the forces that precipitated the crisis at the U.S. Capitol on January 6. But first, because there has been precious little to celebrate in recent months, I want to note some good news:
On Wednesday afternoon, just hours after his inauguration, President Biden issued an executive order fully implementing the Supreme Court's June 2020 decision in Bostock v. Clayton County, which held that the Civil Rights Act of 1964 bars employment discrimination against LGBTQ people. In 2019, the Presiding Bishop and I had the honor of being the lead signers of a friend of the court brief filed with the Supreme Court in the Bostock case. In that brief, we joined more than 720 interfaith clergy and faith leaders in declaring that our religious beliefs compel us to support equal protection under the law for LGBTQ people. Our position, as with all of the public policy positions of the Episcopal Church, was based on the actions of General Convention—in this case, on multiple resolutions dating as far back as 1976.
Although the Supreme Court decision is more than six months old, the previous administration had not implemented it, and so yesterday's executive order marks the first time that LGBTQ people have been assured of the legal protections the court had ordered. This is an enormous victory, and only because it came on such a momentous day has it not been given much attention.
People sometimes ask me about the point of General Convention resolutions on matters of public policy, and even question whether they make any difference. Yesterday, we saw the work and witness of many General Conventions culminate as a longstanding wrong was righted. This week, the Episcopal Church's witness made a difference in moving the United States closer to justice for all of God's children, and for that I give great thanks.
Now, unfortunately, not all of Christianity's recent airtime has been that good. You have probably seen, as I have, the coverage detailing how white Christian nationalism fueled the insurrection at the U.S. Capitol on January 6. Signs, banners and flags carried by the rioters declared allegiance to Jesus and the former president, sometimes conflating them, and pledged fealty to God, guns, and America. One group styled itself after Joshua fighting the Battle of Jericho, marching to make "the walls of corruption crumble." Others described visions from God endorsing their efforts to overturn the results of the presidential election or claimed that their efforts to save America from "tyranny" are inspired by God.
The stories, signs and symbols of our faith are being put to violent use by people who want to establish a nation in which power and privilege is held exclusively by white Christians. This isn't simply a set of policy disagreements between liberals and conservatives, between people who want elected officials to enact laws based on one set of values instead of another. It is domestic terrorism. As author Katherine Stewart said in an interview with Sojourners last March:
…Christian nationalism does not believe in modern, pluralistic democracy. Its aim is to create a new type of order, one in which Christian nationalist leaders, along with members of certain approved religions and their political allies will enjoy positions of exceptional privilege in politics, law, and society. So, this is a political movement and its goal is ultimately power. It doesn't seek to add another voice to America's pluralistic democracy, but rather to place our foundational democratic principles and institutions with a state grounded in a particular version of religion, and what some adherents call a biblical world view.
In these hard days, when our country needs so badly to heal, it is tempting—for me, at least—to look the other way when we encounter Christian nationalists. We're not that kind of Christians, we think. We want to believe that if we just talk across our differences or build relationships with people on the other side of the political divide, we can put this terrible nightmare behind us. We hope and pray that it's over now because the former president is out of office and off of Twitter.
But the use of Christianity to advance white supremacist extremism did not begin in 2016, and it did not end at noon on Wednesday. This violent and exclusionary movement is on the rise in the United States, and those of us who believe that God is calling us toward a very different vision, toward the Beloved Community, have a special responsibility to stand against it. If we will not tell the world that it is not Christianity, then who will?
Last October, the Office of Government Relations (OGR) provided us with a white paper about ways that our church could consider becoming involved in deradicalization efforts that seek to reach those who have joined extremist groups and those who are tempted by them. Other Anglican Communion provinces have taken on this work, so there are models to follow and partners to consult. Here's a passage from the OGR paper:
The Episcopal Church has the opportunity to respond to this threat by offering an "off-ramp" for those who have joined extremism groups, expanding the possibility of reconciliation and forgiveness. The Church can prevent those who are on the brink of joining radical extremist groups from doing so, inoculating young people from succumbing to these ideologies. Many at-risk people still have community connections through churches, whether through friends, families, or community members. With programming in place, clergy and church leaders who are trained in this kind of outreach could help pull young people back into communities and churches.
We didn't give the need for deradicalization work serious attention in October. I suspect that some of us thought that it was an overreaction, or that it might be divisive to suggest that people with different political ideas from ours are dangerous, or that things would calm down after the election. And certainly, I do not mean to suggest that everyone who votes the opposite ticket from mine are thereby enemies of democracy or dangerous terrorists. There have been times in the past when my husband and I have cancelled each other's votes, and we have been married for 44 years. I know with certainty that he is not an extremist; I hope he would say the same about me—at least on most days.
But this issue looks different now, doesn't it? We've seen with our own horrified eyes what Christian nationalism can do to the Capitol, to the Congress, to the country. We know that sickening feeling of seeing the symbols and signs we hold so dear used to justify terror. We've seen our capital city occupied by thousands of troops because of credible threats of violence against our government and feared for the lives of our elected officials.
As Christian leaders who understand that Jesus calls us to live in harmony with all of God's children, I think we need to look again at how we can be agents of peace through the work of deradicalizing those who distort our faith in deadly, destructive ways. I understand that the Joint Standing Committee on Mission Within The Episcopal Church began this conversation at our last meeting, and I hope they will bring a resolution to the floor for us to consider at this meeting so that we can begin to take this idea seriously.
Thank you, as always, for your work on behalf of our beloved church and the communities we serve.
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redpajama_set_name: RedPajamaCommonCrawl


Following the signing of a new executive order by California Governor Jerry Brown, the official target for all-electric vehicle sales in the state is now 5 million electric cars on California's roads by 2030.
Over at CleanTechnica, Steve Hanley reports more details: "To reach the goal, California will spend $2.5 billion between now and 2025 to install more charging stations and hydrogen fueling stations throughout the state. It will also beef up its incentives and rebate programs for people who buy zero emissions cars. Right now, there are about 350,000 zero-emissions vehicles on the road in California. Increasing the number 15 fold in 12 years will be a daunting task.
While this news is of course worth taking consideration of, it remains to be seen what it will amount to in practice. One thing that is certain, however, is that this move will definitely upset the Trump base and his Administration's EPA!
By James Ayre, originally published by EVObsession.


text:
CfP: 1914-1919: Imperial War to Class War
By Administrator on August 11, 2013 in Events & News
Call for papers: 1914-1919: Imperial War to Class War
Institute of Historical Research, WC1, 25th January 2014
Organised by the London Socialist Historians Group
The labour movement internationally supported the First World War but a minority across a range of viewpoints from Keir Hardie to Lenin refused to go along with their Government's warmongering.
The war was to lead to death on an industrial scale and eventually revolution in Russia and Germany.
The Coalition Government plans to mark the 100th anniversary of the start of the war but not as a victory. Many on the right however are demanding that it should be commemorated as such.
This conference will seek to take an alternative look at a range of aspects of WW1 from those who opposed it, to the workers movements which developed during it and after it and the harsh and deathly realities of the 'war to end all wars'.
Papers presenting new research in these areas and perhaps particularly the impact of women and ethnic minorities in the war, which have been and are likely to remain under represented in historical studies, are particularly welcome.
For further information, please visit: http://londonsocialisthistorians.blogspot.co.uk/2013/08/cfp-lshg-conference-on-world-war-one.html
Proposals for papers are invited- 500 words maximum- by the end of September 2013
Please email submissions to Keith Flett


text:
Nathan Lane, Glenda Jackson among Tony snubs as nominations mostly play it safe
By Chris Jones
(L) Glenda Jackson in "King Lear" and (R) Nathan Lane in "Gary". (Handout)
Bryan Cranston can't have been surprised, and anything but mad as hell, after his nod for "Network." But Tuesday was a lousy morning for two other veteran, brand-name thespians: Glenda Jackson ("King Lear") and Nathan Lane ("Gary"), both of whom were unjustly snubbed by the Tony Awards nominating committee.
And for Laurie Metcalf, the Tony nominations morning must have been as routine as grabbing a cup of coffee: Incredibly, the former "Roseanne" cast member and current acerbic star of "Hillary and Clinton" was nominated for the fourth consecutive year.
As Broadway looks for a safe landing between changing times and the traditional desires of its mostly affluent and older audience, this year's Tony nominations reflected fevered competition between more traditional productions and radical reimagines of what constitutes a Broadway show. The Tony nominators mostly played it safe and landed in the middle.
Take the best-musical category: "Tootsie" (old-school adaptation of a movie) and "Hadestown" (edgy score and political lyrics by Anais Mitchell) will go head to head, with "Ain't Too Proud" (the traditional Temptations jukebox) and "The Prom" (a progressive caper show about a big gay prom in Indiana) both capable of spoiling the party. "Hadestown" takes far more risks and has the greatest level of artistry — but its appeal is primarily to urbanite progressives, while "Tootsie" will play in red-and-blue-state America.
Surprisingly, the profane and acerbic "Beetlejuice," hardly a critic's favorite, also appeared in the category at the expense of the sweeter high-school favorite, "Be More Chill," which had to be chill with a nod for best score. Kids across the country took to social media to lambaste the old has-beens on the Tony committee.
[More Broadway] 'Waitress' is closing on Broadway after nearly four years »
Under musical revivals, meanwhile, Scott Ellis' mostly old-school and warm-centered re-staging of "Kiss Me Kate" will go head head-to-head with Daniel Fish's radical deconstruction of "Oklahoma," a shocking production that nixed the usual romantic emphasis on love, marriage and optimism in favor of an indictment of conflict-ridden settlers who belong to the land only in their own heads.
The 2019 Tony Award Nominees
In a very strong year for plays, the favorite will be "The Ferryman," the Jez Butterworth epic about the Irish "troubles." Also in that competitive category: Taylor Mac's bizarre "Gary," James Graham's Rupert Murdoch-baiting epic "Ink," Tarell Alvin McCraney's earnest "Choir Boy" and Heidi Schreck's intensely personal piece, "What the Constitution Means to Me."
In another surprise, there was no best new play spot for Aaron Sorkin's radical retelling of Harper Lee's "To Kill a Mockingbird," even though it (a) clearly was a new play and (b) is selling about as many tickets as all the other new plays combined. Among revivals, the main competition is likely to be between "All My Sons" and "The Waverly Gallery," with "Torch Song," "The Boys in the Band" and "Burn This" filling out the slate. There was no spot for "King Lear."
[More Broadway] Controversial 'Slave Play' headed to Broadway this fall; ex-Lady Gaga manager and Disney heiress to produce »
Stephanie J. Block scored her expected nomination for playing Cher, with all the attitudes, in "The Cher Show." In the category of best actress in a musical, she'll be up against Beth Leavel ("The Prom"), Kelli O'Hara ("Kiss Me Kate"), Eva Noblezada ("Hadestown"), and Caitlin Kinnunen ("The Prom"). It's hard to see anyone blocking Cher.
Santino Fontana is the favorite to win the best actor in a musical Tony for his work as the lead character in "Tootsie," an adaptation of the beloved movie about an actor who pretends to be a woman to get more work. He'll compete with Damon Daunno ("Oklahoma! "), Brooks Ashmanskas ("The Prom"), Derrick Baskin ("AIn't Too Proud") and Alex Brightman, the lead nasty in the much-maligned "Beetlejuice."
In the best actor in a play category, Cranston will be the favorite, with Jeff Daniels ("To Kill a Mockingbird") offering some very strong competition with Paddy Consadine ("The Ferryman") also making a case for himself. Among actresses in a play, the octogenarian Elaine May ("The Waverly Gallery") and Laurie Metcalf ("Hillary and Clinton") are the strongest competitors, although you can't count out either Shrek or Annette Benning, both unselfish and generally terrific in "All My Sons."
[More Broadway] Neil Diamond biographical musical headed to Broadway »
This year's Tony Awards are scheduled for June 9 at the Radio City Music Hall. Bebe Neuwirth and Brandon Victory Dixon are the presenters.
A full list of nominees appears below.
[More Broadway] 'Moulin Rouge' to Shakespeare: Every on and Off-Broadway show to check out this summer »
"Ain't Too Proud - The Life and Times of The Temptations"
"Beetlejuice"
"Hadestown"
[More Broadway] 'The Cher Show' and 'King Kong' closing on Broadway after less than a year »
"The Prom"
"Tootsie"
[More Broadway] 'Will & Grace' star Debra Messing returning to Broadway in 'Birthday Candles' »
"Choir Boy" by Tarell Alvin McCraney
"The Ferryman" by Jez Butterworth
"Gary: A Sequel to Titus Andronicus" by Taylor Mac
[More Broadway] Back on Broadway: 23 years after last role, Ed Harris set to replace Jeff Daniels in Aaron Sorkin's 'To Kill A Mockingbird' adaptation »
"Ink" by James Graham
"What the Constitution Means to Me" by Heidi Schreck
Best Revival of a Musical
[More Broadway] 'Hadestown' wins Tony for best musical, 'The Ferryman' named best play, and Elaine May wins her first acting Tony at age 87 in star-studded Radio City award show »
"Kiss Me, Kate"
"Rodgers and Hammerstein's Oklahoma!"
Best Revival of a Play
[More Broadway] Strong Broadway season gives Tony voters plenty of diverse options »
Arthur Miller's "All My Sons"
"The Boys in the Band" by Mart Crowley
"Burn This"
[More Broadway] REVIEW: Broadway revival of Terrence McNally's 'Frankie and Johnny in the Claire de Lune' remains moving look at love and loneliness »
"Torch Song" by Harvey Fierstein
"The Waverly Gallery" by Kenneth Lonergan
Best Performance by an Actor in a Leading Role in a Musical
[More Broadway] 'Grey's Anatomy' heartthrob Jesse Williams set to make Broadway debut in 'Take Me Out,' racially-charged drama about gay professional baseball player »
Brooks Ashmanskas, "The Prom"
Derrick Baskin, "Ain't Too Proud"
Alex Brightman, "Beetlejuice"
[More Broadway] A Tony Award family affair: Lilli Cooper, a nominee for 'Tootsie,' can win same honor as her dad, Chuck »
Damon Daunno, "Oklahoma!"
Santino Fontana, "Tootsie"
Best Performance by an Actress in a Leading Role in a Musical
Stephanie J. Block, "The Cher Show"
Caitlin Kinnunen, "The Prom"
Beth Leavel, "The Prom"
[More Broadway] REVIEW: Disjointed, manic 'Beetlejuice' musical is a hard show to swallow »
Eva Noblezada, "Hadestown"
Kelli O'Hara, "Kiss Me, Kate"
Best Performance by an Actor in a Leading Role in a Play
[More Broadway] Broadway 'Beetlejuice' actress who plays Lydia is just as quirky as her death-obsessed character »
Paddy Considine, "The Ferryman"
Bryan Cranston, "Network"
Jeff Daniels, "To Kill a Mockingbird"
[More Broadway] REVIEW: Broadway's 'Ink' is juicy, colorful tale about the rise of right-wing media mogul Rupert Murdoch »
Adam Driver, "Burn This"
Jeremy Pope, "Choir Boy"
Best Performance by an Actress in a Leading Role in a Play
[More Broadway] REVIEW: Broadway musical take on 'Tootsie' keeps laughs rolling even as it deconstructs the 1982 movie »
Annette Bening, "All My Sons"
Laura Donnelly, "The Ferryman"
Elaine May, "The Waverly Gallery"
[More Broadway] Beetlejuice takes a back seat to goth girl Lydia in Broadway musical version of hit film »
Janet McTeer, "Bernhardt/Hamlet"
Laurie Metcalf, "Hillary and Clinton"
Heidi Schreck, "What the Constitution Means to Me"
[More Broadway] REVIEW: Broadway revival of Arthur Miller's timeless 'All My Sons' reflects today's contradictory demands of a free market and ethical behavior »
Best Book of a Musical
"Ain't Too Proud," Dominique Morisseau
"Beetlejuice," Scott Brown and Anthony King
[More Broadway] REVIEW: Nathan Lane plays title character in Broadway's 'Gary: A Sequel to Titus Andronicus' with a funny, formidable ferocity »
"Hadestown," Anaïs Mitchell
"The Prom," Bob Martin and Chad Beguelin
"Tootsie," Robert Horn
[More Broadway] REVIEW: Broadway's 'Hillary and Clinton' is a clever, complex black comedy on the unique dynamic between former first couple »
Best Original Score (Music and/or Lyrics) Written for the Theatre
"Be More Chill," Joe Iconis
"Beetlejuice," Eddie Perfect
[More Broadway] REVIEW: 'Hadestown' is a relevant and resistant Broadway musical for the Age of Trump »
"The Prom," Matthew Sklar and Chad Beguelin
"To Kill a Mockingbird," Adam Guettel
[More Broadway] REVIEW: Broadway revival of Lanford Wilson's searing ′Burn/This' needs more sizzle despite appealing cast »
"Tootsie," David Yazbek
Best Direction of a Musical
Rachel Chavkin, "Hadestown"
[More Broadway] 'Tina Turner Musical' gets opening date on Broadway »
Scott Ellis, "Tootsie"
Daniel Fish, "Oklahoma!"
Des McAnuff, "Ain't Too Proud"
[More Broadway] REVIEW: Broadway revival of 'Oklahoma!' stands as brilliant metaphor for our current condition as a nation divided »
Casey Nicholaw, "The Prom"
Best Direction of a Play
Rupert Goold, "Ink"
[More Broadway] REVIEW: Glenda Jackson is extraordinary as Shakespeare's mad monarch in uneven production of 'King Lear' »
Sam Mendes, "The Ferryman"
Bartlett Sher, "To Kill a Mockingbird"
Ivo van Hove, "Network"
[More Broadway] REVIEW: Broadway's 'What the Constitution Means to Me' melds radical constitutional theory with genuine warmth and humor »
George C. Wolfe, "Gary: A Sequel to Titus Andronicus"
Best Performance by an Actor in a Featured Role in a Musical
Andre De Shields, "Hadestown"
[More Broadway] 'Ain't Too Proud,' the tale of The Temptations, needed to tell its own story »
Andy Grotelueschen, "Tootsie"
Patrick Page, "Hadestown"
Jeremy Pope, "Ain't Too Proud"
[More Broadway] James Corden is hosting the 2019 Tony Awards »
Ephraim Sykes, "Ain't Too Proud"
Best Performance by an Actress in a Featured Role in a Musical
Lilli Cooper, "Tootsie"
[More Broadway] REVIEW: 'Kiss Me Kate' on Broadway makes for a pleasurable evening in the company of seasoned theater pros »
Amber Gray, "Hadestown"
Sarah Stiles, "Tootsie"
Ali Stroker, "Oklahoma!"
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Mary Testa, "Oklahoma!"
Best Performance by an Actor in a Featured Role in a Play
Bertie Carvel, "Ink"
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Robin De Jesús, "The Boys in the Band"
Gideon Glick, "To Kill a Mockingbird"
Brandon Uranowitz, "Burn This"
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Benjamin Walker , "All My Sons"
Best Performance by an Actress in a Featured Role in a Play
Fionnula Flanagan, "The Ferryman"
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Celia Keenan-Bolger, "To Kill a Mockingbird"
Kristine Nielsen, "Gary: A Sequel to Titus Andronicus"
Julie White, "Gary: A Sequel to Titus Andronicus"
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Ruth Wilson, "King Lear"
Camille A. Brown, "Choir Boy"
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Warren Carlyle, "Kiss Me, Kate"
Denis Jones, "Tootsie"
David Neumann, "Hadestown"
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Sergio Trujillo, "Ain't Too Proud"
Best Orchestrations
Michael Chorney and Todd Sickafoose, "Hadestown"
[More Broadway] THEATER REVIEW: 'The Cher Show' uses a trifecta of Chers to turn back time on the diva's life and career »
Larry Hochman, "Kiss Me, Kate"
Daniel Kluger, "Oklahoma!"
Simon Hale, "Tootsie"
[More Broadway] Kanye West blasted by Broadway actor for being on his phone during 'The Cher Show' opening night »
Harold Wheeler, "Ain't Too Proud"
Best Scenic Design of a Musical
Robert Brill and Peter Nigrini, "Ain't Too Proud"
[More Broadway] How Chaz Bono's gender as a child is addressed in Broadway's 'The Cher Show' »
Peter England, "King Kong"
Rachel Hauck, "Hadestown"
Laura Jellinek, "Oklahoma!"
[More Broadway] Why Sonny Bono may have avoided Broadway's 'The Cher Show' if he were alive »
David Korins, "Beetlejuice"
Best Scenic Design of a Play
Miriam Buether, "To Kill a Mockingbird"
[More Broadway] REVIEW: Broadway saves Indiana in 'The Prom,' a savvy, self-aware and consistently funny new musical of liberal longing »
Bunny Christie, "Ink"
Rob Howell, "The Ferryman"
Santo Loquasto, "Gary: A Sequel to Titus Andronicus"
[More Broadway] 'King Kong': Spectacular giant puppet can't make up for lack of complex characters and cohesive music »
Jan Versweyveld, "Network"
Best Costume Design of a Musical
Michael Krass, "Hadestown"
[More Broadway] This is 'King Kong' on Broadway's most important lesson according to its star »
William Ivey Long, "Beetlejuice"
William Ivey Long, "Tootsie"
Bob Mackie, "The Cher Show"
[More Broadway] Catch free Broadway musical performances from 'Mean Girls,' 'Wicked,' 'Kinky Boots' and more »
Paul Tazewell, "Ain't Too Proud"
Best Costume Design of a Play
[More Broadway] 'American Son' on Broadway: Kerry Washington unpacks a mother's terror »
Toni-Leslie James, "Bernhardt/Hamlet"
Clint Ramos, "Torch Song"
Ann Roth, "Gary: A Sequel to Titus Andronicus"
[More Broadway] What it's like starring opposite King Kong on Broadway — and being a black actress in a role historically played by blonds »
Ann Roth, "To Kill a Mockingbird"
Best Sound Design of a Musical
Peter Hylenski, "Beetlejuice"
[More Broadway] 'Torch Song' on Broadway: Gay life in the '80s, when you couldn't even trust your mom »
Peter Hylenski, "King Kong"
Steve Canyon Kennedy, "Ain't Too Proud"
Drew Levy, "Oklahoma!"
[More Broadway] The Waverly Gallery: Elaine May, falling apart on Broadway and showing us our future »
Nevin Steinberg and Jessica Paz, "Hadestown"
Best Sound Design of a Play
Adam Cork, "Ink"
[More Broadway] THEATER REVIEW: In 'The Ferryman,' actors, real animals and a Iive human baby fight their epic destiny »
Scott Lehrer, "To Kill a Mockingbird"
Fitz Patton, "Choir Boy"
Nick Powell, "The Ferryman"
[More Broadway] REVIEW: In 'The Lifespan of a Fact' on Broadway, Daniel Radcliffe rails against truthiness »
Eric Sleichim, "Network"
Best Lighting Design of a Musical
Kevin Adams , "The Cher Show"
[More Broadway] Laurie Metcalf, John Lithgow to star in 'Hillary and Clinton' on Broadway »
Howell Binkley, "Ain't Too Proud"
Bradley King, "Hadestown"
Peter Mumford, "King Kong"
[More Broadway] 'Almost Famous' to become a stage musical that may come to Broadway »
Kenneth Posner and Peter Nigrini, "Beetlejuice
Best Lighting Design of a Play
Neil Austin, "Ink"
[More Broadway] Harvard's Hasty Pudding theater club casts 6 women after 175 years of all-male shows »
Jules Fisher and Peggy Eisenhauer, "Gary: A Sequel to Titus Andronicus"
Peter Mumford, "The Ferryman"
Jennifer Tipton, "To Kill a Mockingbird"
Jan Versweyveld and Tal Yarden, "Network"
Carole King musical 'Beautiful' closing on Broadway after six years


FLCC provides hands-on service learning opportunities designed to develop leaders in the fields of land management, cultural preservation, resource based recreation and park facility management.
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text:
Q: Can program crashes during development affect my system's security? I have been using Ubuntu for some time, and I loved it! I'm feeling way more safe now.
But, I'm a Computer Science Student, and I have to code a lot. And I have been creating various codes, and it caused a lot of Segmentation faults, stack overflows, stack smashes, etc.
I have been wondering, does this errors can cause any harm to the memory of the OS or creating something like a bug?

A: A program runs in a especially allocated space in memory. A segfault, stack overflow, etc. happens inside this space.
When you run your programs normally, these errors won't affect anything else. All these errors happen on the RAM btw., not on persistent memory.
So you won't compromise your computer with stuff like this. (Unless you're doing some buggy file I/O as root..., which you probably shouldn't during development)

redpajama_set_name: RedPajamaStackExchange


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text:
Wenn der Anker fällt ist das zweite Musikalbum des deutschen Schlagersängers Olaf Malolepski, der durch die ehemalige Schlagergruppe Die Flippers bekannt wurde. Es wurde am 12. Oktober 2012 in Deutschland, Österreich und der Schweiz durch Ariola (Sony Music) veröffentlicht.

Entstehung
Im August 2012 gab Malolepski auf seiner Facebook-Seite bekannt, dass am 12. Oktober 2012 ein neues Album mit dem Namen Wenn der Anker fällt erscheinen werde.

Die 14 Titel wurden von Joschi Dinier, Oliver Corvino, Armin Kandel, Frank Becker, Marcel Brell, Reiner Burmann, Andreas Bärtels, Werner Stephan und Anke Thomas komponiert. Die Texte stammen unter anderem von Joschi Dinier, Tommy de Winter, Helmut Theil, Marita Theil, Tobias Reitz, Edith Jeske, Frank Becker, Matthias Teriet, Bernd Meinunger. Arrangeure waren Joschi Dinier und Reiner Burmann. Produziert wurde das Album von Joschi Dinier, wie schon beim Debütalbum. Beim Titel Sag mir wie weit fliegen die Träume wirkte seine Tochter Pia Malo mit.

Covergestaltung
Auf dem Cover ist Malolepski in einem blauen Anzug zu sehen. Sein Name und der Albumtitel sind mit goldener Farbe geschrieben. Im Hintergrund sieht man ein Wellenmeer.

Musikstil
Ebenfalls wie beim Debütalbum gibt es wenige Unterschiede zum Musikstil der Flippers. Themen sind die Liebe und Glück. Gelegentlich werden auch nachdenkliche Töne angesprochen.

Titelliste
 Wenn der Anker fällt
 Bitte hör nie auf mit mir zu träumen
 Du tust mir gut
 Komm doch mit auf meine Insel
 Eine Sekunde tausend Gefühle
 Sag mir wie weit fliegen die Träume (mit Tochter Pia Malo)
 Alegria
 "C'est la vie"
 Das kann doch keine Sünde sein
 Irgendwie vermisse ich Euch
 Die Frau aus meinen Träumen
 Sehnsucht kommt ganz leise
 Wunderbar
 Mein Lied für Euch

Charts und Chartplatzierungen

Weblinks

 Wenn der Anker fällt bei Musicline.de

Einzelnachweise

Album 2012
Album (Schlager)

redpajama_set_name: RedPajamaWikipedia