Nucleosome-coupled expression differences in closely-related species

<p>Abstract</p> <p>Background</p> <p>Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate t...

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Main Authors: Gebbia Marinella, Tsui Kyle, Yao Victoria, Guan Yuanfang, Dunham Maitreya J, Nislow Corey, Troyanskaya Olga G
Format: Article
Language:English
Published: BMC 2011-09-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/12/466
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author Gebbia Marinella
Tsui Kyle
Yao Victoria
Guan Yuanfang
Dunham Maitreya J
Nislow Corey
Troyanskaya Olga G
author_facet Gebbia Marinella
Tsui Kyle
Yao Victoria
Guan Yuanfang
Dunham Maitreya J
Nislow Corey
Troyanskaya Olga G
author_sort Gebbia Marinella
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p>Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown.</p> <p>Results</p> <p>We address this challenge by generating nucleosome positioning and cell cycle expression data for <it>Saccharomyces bayanus </it>and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, <it>S. bayanus </it>and <it>S. cerevisiae</it>. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs).</p> <p>Conclusions</p> <p>Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.</p>
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spelling doaj.art-85024de2a68945bca7e0b7c99203573e2022-12-21T21:03:22ZengBMCBMC Genomics1471-21642011-09-0112146610.1186/1471-2164-12-466Nucleosome-coupled expression differences in closely-related speciesGebbia MarinellaTsui KyleYao VictoriaGuan YuanfangDunham Maitreya JNislow CoreyTroyanskaya Olga G<p>Abstract</p> <p>Background</p> <p>Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown.</p> <p>Results</p> <p>We address this challenge by generating nucleosome positioning and cell cycle expression data for <it>Saccharomyces bayanus </it>and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, <it>S. bayanus </it>and <it>S. cerevisiae</it>. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs).</p> <p>Conclusions</p> <p>Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.</p>http://www.biomedcentral.com/1471-2164/12/466
spellingShingle Gebbia Marinella
Tsui Kyle
Yao Victoria
Guan Yuanfang
Dunham Maitreya J
Nislow Corey
Troyanskaya Olga G
Nucleosome-coupled expression differences in closely-related species
BMC Genomics
title Nucleosome-coupled expression differences in closely-related species
title_full Nucleosome-coupled expression differences in closely-related species
title_fullStr Nucleosome-coupled expression differences in closely-related species
title_full_unstemmed Nucleosome-coupled expression differences in closely-related species
title_short Nucleosome-coupled expression differences in closely-related species
title_sort nucleosome coupled expression differences in closely related species
url http://www.biomedcentral.com/1471-2164/12/466
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AT tsuikyle nucleosomecoupledexpressiondifferencesincloselyrelatedspecies
AT yaovictoria nucleosomecoupledexpressiondifferencesincloselyrelatedspecies
AT guanyuanfang nucleosomecoupledexpressiondifferencesincloselyrelatedspecies
AT dunhammaitreyaj nucleosomecoupledexpressiondifferencesincloselyrelatedspecies
AT nislowcorey nucleosomecoupledexpressiondifferencesincloselyrelatedspecies
AT troyanskayaolgag nucleosomecoupledexpressiondifferencesincloselyrelatedspecies