Next Article in Journal
Intrinsic Properties of tRNA Molecules as Deciphered via Bayesian Network and Distribution Divergence Analysis
Previous Article in Journal
Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles
Article Menu

Export Article

Open AccessArticle

The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis

Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany
*
Author to whom correspondence should be addressed.
Received: 23 December 2017 / Revised: 25 January 2018 / Accepted: 25 January 2018 / Published: 30 January 2018
(This article belongs to the Special Issue Evolution and Origin of Genomes)
View Full-Text   |   Download PDF [4367 KB, uploaded 30 January 2018]   |  

Abstract

The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or “CTCF-like” (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach. We find that CTCF has 52 direct interaction partners while CTCFL only has 19. Almost all interactors already existed before the emergence of CTCF and CTCFL. The unique secondary loss of CTCF from several nematodes is paralleled by a loss of two of its interactors, the polycomb repressive complex subunit SuZ12 and the multifunctional transcription factor TYY1. In contrast to earlier studies reporting the absence of BORIS from birds, we present evidence for a multigene synteny block containing CTCFL that is conserved in mammals, reptiles, and several species of birds, indicating that not the entire lineage of birds experienced a loss of CTCFL. Within this synteny block, BORIS and its genomic neighbors seem to be partitioned into two nested chromatin loops. The high expression of SPO11, RAE1, RBM38, and PMEPA1 in male tissues suggests a possible link between CTCFL, meiotic recombination, and fertility-associated phenotypes. Using the 65,700 exomes and the 1000 genomes data, we observed a higher number of intergenic, non-synonymous, and loss-of-function mutations in CTCFL than in CTCF, suggesting a reduced strength of purifying selection, perhaps due to less functional constraint. View Full-Text
Keywords: CTCF; gene duplication; chromatin loops; polymorphism; natural selection; Bilateria; Amniotes CTCF; gene duplication; chromatin loops; polymorphism; natural selection; Bilateria; Amniotes
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Share & Cite This Article

MDPI and ACS Style

Jabbari, K.; Heger, P.; Sharma, R.; Wiehe, T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life 2018, 8, 4.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Life EISSN 2075-1729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top
{"cc_re__cc_re__cc_by_3_0": ["      <meta name=\"dc.creator\" content=\"Peter Heger\">\n            <meta name=\"dc.creator\" content=\"Ranu Sharma\">\n            <meta name=\"dc.creator\" content=\"Thomas Wiehe\">\n    \n    <meta name=\"dc.type\" content=\"Article\">\n    <meta name=\"dc.source\" content=\"Life 2018, Vol. 8, Page 4\">\n    <meta name=\"dc.date\" content=\"2018-01-30\">\n            <meta name =\"dc.identifier\" content=\"10.3390/life8010004\">\n    \n    <meta name=\"dc.publisher\" content=\"Multidisciplinary Digital Publishing Institute\">\n    <meta name=\"dc.rights\" content=\"http://creativecommons.org/licenses/by/3.0/\">\n    <meta name=\"dc.format\" content=\"application/pdf\" >\n    <meta name=\"dc.language\" content=\"en\" >\n\t<meta name=\"dc.description\" content=\"The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called \u201cBrother of Regulator of Imprinted Sites\u201d (BORIS) or \u201cCTCF-like\u201d (CTCFL). It binds DNA at "], "cc_re__cc_re__cc_by_4_0": ["         &lt;p&gt;Histogram showing enrichment for mutations in CTCF(L) based on the 1000 genomes phase 3 data. The y-axis displays the ratio of the normalized number of mutations in CTCFL and CTCF (r = N&lt;sub&gt;CTCFL&lt;/sub&gt;/N&lt;sub&gt;CTCF&lt;/sub&gt;).&lt;/p&gt;\n                                                            \"></a></div>\n\t\t\t\n\t\t\t<div class=\"licenseText in-tab\" style=\"padding: 1em 0;\">\n                                    This is an open access article distributed under the <a href=\"https://creativecommons.org/licenses/by/4.0/\" target=\"_blank\">Creative Commons Attribution License</a> which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).\n                \t\t\t</div>\n\n\t   </div>\n\n\t\t\t\t<div id=\"tabs-4\" class=\"ui-tabs-panel\">\n\t\t\t<a id=\"suppl_id\" name=\"supplementary\"></a>\n\t\t\t<h1>Supplementary material</h1>\n\t\t\t\t\t\t\n\t\t\t<div class=\"in-tab\">\n\t\t\t\t<ul style=\"margin:0; list-style: none;\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<li><a name=\"supplementary_file1\"></a><b>Supplemen"], "copyright__copyright__copyright": ["ma, R.; Wiehe, T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life 2018, 8, 4.\n\nShow more citation formats Show less citations formats\n\nNote that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.\n\nRelated Articles\n\nArticle Metrics\n\nArticle Access Statistics\n\n1\n\nComments\n\n[Return to top]\nLife EISSN 2075-1729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert\nBack to Top", "ma, R.; Wiehe, T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life 2018, 8, 4.\n\nShow more citation formats Show less citations formats\n\nNote that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.\n\nRelated Articles\n\nArticle Metrics\n\nArticle Access Statistics\n\n1\n\nComments\n\n[Return to top]\nLife EISSN 2075-1729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert\nBack to Top", "ma, R.; Wiehe, T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life 2018, 8, 4.\n\nShow more citation formats Show less citations formats\n\nNote that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.\n\nRelated Articles\n\nArticle Metrics\n\nArticle Access Statistics\n\n1\n\nComments\n\n[Return to top]\nLife EISSN 2075-1729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert\nBack to Top"]}