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Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlyi...
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817486/ https://www.ncbi.nlm.nih.gov/pubmed/19933262 http://dx.doi.org/10.1093/nar/gkp989 |
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author | Singh, Larry N. Hannenhalli, Sridhar |
author_facet | Singh, Larry N. Hannenhalli, Sridhar |
author_sort | Singh, Larry N. |
collection | PubMed |
description | Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlying expression divergence are not completely understood, transcription factor binding sites and nucleosome occupancy are known to play a significant role in the process. Previous attempts to detect genomic variations mediating expression divergence in orthologs have had limited success for two primary reasons. First, it is inherently challenging to compare expressions among orthologs due to variable trans-acting effects and second, previous studies have quantified expression divergence in terms of an overall similarity of expression profiles across multiple samples, thereby obscuring condition-specific expression changes. Moreover, the inherently inter-correlated expressions among homologs present statistical challenges, not adequately addressed in many previous studies. Using rigorous statistical tests, here we characterize the relationship between cis element divergence and condition-specific expression divergence among paralogous genes in Saccharomyces cerevisiae. In particular, among all combinations of gene family and TFs analyzed, we found a significant correlation between TF binding and the condition-specific expression patterns in over 20% of the cases. In addition, incorporating nucleosome occupancy reveals several additional correlations. For instance, our results suggest that GAL4 binding plays a major role in the expression divergence of the genes in the sugar transporter family. Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions. |
format | Text |
id | pubmed-2817486 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-28174862010-02-08 Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families Singh, Larry N. Hannenhalli, Sridhar Nucleic Acids Res Gene Regulation, Chromatin and Epigenetics Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlying expression divergence are not completely understood, transcription factor binding sites and nucleosome occupancy are known to play a significant role in the process. Previous attempts to detect genomic variations mediating expression divergence in orthologs have had limited success for two primary reasons. First, it is inherently challenging to compare expressions among orthologs due to variable trans-acting effects and second, previous studies have quantified expression divergence in terms of an overall similarity of expression profiles across multiple samples, thereby obscuring condition-specific expression changes. Moreover, the inherently inter-correlated expressions among homologs present statistical challenges, not adequately addressed in many previous studies. Using rigorous statistical tests, here we characterize the relationship between cis element divergence and condition-specific expression divergence among paralogous genes in Saccharomyces cerevisiae. In particular, among all combinations of gene family and TFs analyzed, we found a significant correlation between TF binding and the condition-specific expression patterns in over 20% of the cases. In addition, incorporating nucleosome occupancy reveals several additional correlations. For instance, our results suggest that GAL4 binding plays a major role in the expression divergence of the genes in the sugar transporter family. Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions. Oxford University Press 2010-01 2009-11-19 /pmc/articles/PMC2817486/ /pubmed/19933262 http://dx.doi.org/10.1093/nar/gkp989 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene Regulation, Chromatin and Epigenetics Singh, Larry N. Hannenhalli, Sridhar Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
title | Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
title_full | Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
title_fullStr | Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
title_full_unstemmed | Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
title_short | Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
title_sort | correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families |
topic | Gene Regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817486/ https://www.ncbi.nlm.nih.gov/pubmed/19933262 http://dx.doi.org/10.1093/nar/gkp989 |
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