Cargando…
Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila
BACKGROUND: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419465/ https://www.ncbi.nlm.nih.gov/pubmed/25887553 http://dx.doi.org/10.1186/s12864-015-1495-3 |
_version_ | 1782369579444469760 |
---|---|
author | Carl, Sarah H Russell, Steven |
author_facet | Carl, Sarah H Russell, Steven |
author_sort | Carl, Sarah H |
collection | PubMed |
description | BACKGROUND: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known. RESULTS: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species. CONCLUSION: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1495-3) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4419465 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-44194652015-05-06 Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila Carl, Sarah H Russell, Steven BMC Genomics Research Article BACKGROUND: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known. RESULTS: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species. CONCLUSION: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1495-3) contains supplementary material, which is available to authorized users. BioMed Central 2015-04-13 /pmc/articles/PMC4419465/ /pubmed/25887553 http://dx.doi.org/10.1186/s12864-015-1495-3 Text en © Carl and Russell; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Carl, Sarah H Russell, Steven Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila |
title | Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila |
title_full | Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila |
title_fullStr | Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila |
title_full_unstemmed | Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila |
title_short | Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila |
title_sort | common binding by redundant group b sox proteins is evolutionarily conserved in drosophila |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419465/ https://www.ncbi.nlm.nih.gov/pubmed/25887553 http://dx.doi.org/10.1186/s12864-015-1495-3 |
work_keys_str_mv | AT carlsarahh commonbindingbyredundantgroupbsoxproteinsisevolutionarilyconservedindrosophila AT russellsteven commonbindingbyredundantgroupbsoxproteinsisevolutionarilyconservedindrosophila |