The role of nucleosome positioning in the evolution of gene regulation.

PLoS Biology
Alexander M TsankovOliver J Rando

Abstract

Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs. However, it can be difficult to decipher the basis of changes in chromatin organization and their functional effect on gene expression. Here, we present a large-scale comparative genomic analysis of the relationship between chromatin organization and gene expression, by measuring mRNA abundance and nucleosome positions genome-wide in 12 Hemiascomycota yeast species. We found substantial conservation of global and functional chromatin organization in all species, including prominent nucleosome-free regions (NFRs) at gene promoters, and distinct chromatin architecture in growth and stress genes. Chromatin organization has also substantially diverged in both global quantitative features, such as spacing between adjacent nucleosomes, and in functional groups of genes. Expression levels, intrinsic anti-nucleosomal sequences, and trans-acting chromatin modifiers all play important, complementary, and evolvable roles in determining NFRs. We identify five mechanisms that couple chromatin organization to evolution of gene regulation and have contributed to the evolution of respiro-fermentation and other...Continue Reading

Associated Datasets

Jul 6, 2010·Alex M TsankovAlexander Tsankov
Jul 6, 2010·Aviv RegevAlex M Tsankov
Jul 6, 2010·Alexander TsankovOliver Rando
Jul 6, 2010·Alexander TsankovAlex M Tsankov
Jul 6, 2010·Alex M TsankovAlexander Tsankov
Jul 6, 2010·Alexander TsankovAlex M Tsankov
Jul 6, 2010·Alexander TsankovAlex M Tsankov
Jul 6, 2010·Alexander TsankovAviv Regev

References

Apr 11, 1975·Science·M C King, A C Wilson
Jul 25, 1988·Nucleic Acids Research·R D Kornberg, L Stryer
Dec 20, 1985·Journal of Molecular Biology·H R Drew, A A Travers
Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
Dec 5, 2000·Molecular Biology of the Cell·A P GaschP O Brown
Dec 26, 2001·Nucleic Acids Research·H W MewesB Weil
Mar 30, 2002·Science·Rachel B BremLeonid Kruglyak
Apr 5, 2002·Genome Research·W James Kent
Oct 9, 2002·Proceedings of the National Academy of Sciences of the United States of America·Roy M WilliamsRochelle E Esposito
Dec 19, 2003·Nucleic Acids Research·M A HarrisUNKNOWN Gene Ontology Consortium
Feb 19, 2004·Nature Reviews. Genetics·Harley H McAdamsAdam P Arkin
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Nov 10, 2004·PLoS Biology·Audrey P GaschMichael B Eisen
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Amos TanayRon Shamir
Jun 18, 2005·Science·Guo-Cheng YuanOliver J Rando
Oct 26, 2005·Nucleic Acids Research·Peter D KarpNúria López-Bigas
Dec 31, 2005·Nucleic Acids Research·Kevin P Byrne, Kenneth H Wolfe
Mar 9, 2006·BMC Bioinformatics·Kenzie D MacIsaacErnest Fraenkel
Jun 20, 2006·Nature Genetics·Itay TiroshNaama Barkai
Aug 22, 2006·Nature Reviews. Genetics·Philipp KhaitovichSvante Pääbo
Sep 14, 2006·Proceedings of the National Academy of Sciences of the United States of America·Su-In LeeDaphne Koller
Feb 27, 2007·Cell·Bing LiJerry L Workman
Apr 10, 2007·Trends in Genetics : TIG·Itay TiroshNaama Barkai
May 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Benjamin Prud'hommeSean B Carroll
Aug 2, 2007·Molecular Systems Biology·Gavin C Conant, Kenneth H Wolfe
Mar 3, 1989·Science·R T Simpson
Dec 14, 2007·Nature·Iestyn WhitehouseToshio Tsukiyama
Jan 17, 2008·Molecular Systems Biology·Itay TiroshNaama Barkai
Feb 29, 2008·PLoS Biology·Brian B TuchAlexander D Johnson
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
Mar 18, 2008·Molecular Cell·Hervé HoguesMalcolm Whiteway
Apr 1, 2008·Eukaryotic Cell·Héloïse MullerCécile Fairhead
Apr 15, 2008·Nature·Travis N MavrichB Franklin Pugh
Apr 18, 2008·Nature·Felix H LamErin K O'Shea
May 2, 2008·Genome Research·Itay Tirosh, Naama Barkai

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Citations

Jul 6, 2014·PLoS Genetics·Caitlin F ConnellyJoshua M Akey
Nov 2, 2013·Bioinformatics·Jung-Hsien Chiang, Chan-Hsien Lin
Mar 4, 2014·Nucleic Acids Research·Oscar FloresModesto Orozco
Apr 8, 2014·Annual Review of Biophysics·Amanda L Hughes, Oliver J Rando
Jun 26, 2013·ELife·Dawn A ThompsonAviv Regev
Sep 24, 2010·Nucleic Acids Research·Dong DongZhaolei Zhang
Nov 17, 2010·PLoS Genetics·Ben Lehner
Dec 24, 2010·Genome Research·Sevinç ErcanJason D Lieb
Jan 5, 2011·PLoS Computational Biology·Ephraim KenigsbergAmos Tanay
Jun 8, 2011·Microbiology and Molecular Biology Reviews : MMBR·An Jansen, Kevin J Verstrepen
Sep 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Itay TiroshKevin Struhl
Sep 29, 2011·BMC Genomics·Yuanfang GuanOlga G Troyanskaya
Oct 4, 2011·Molecular Biology and Evolution·Zhenguo Lin, Wen-Hsiung Li
Feb 22, 2012·Genetics·Oliver J Rando, Fred Winston
Jun 6, 2012·Genome Research·Sara C Di RienziBonita J Brewer
Jun 19, 2012·Nature Reviews. Genetics·Irene Gallego RomeroYoav Gilad
Jun 22, 2012·PLoS Genetics·Elizabeth K Engle, Justin C Fay
Sep 29, 2012·Genome Biology and Evolution·Janna L Fierst, Patrick C Phillips
Jan 18, 2013·BMC Genomics·Yuanfang GuanAmy A Caudy
Jan 29, 2013·Genome Biology and Evolution·Nicolas AgierGilles Fischer
Jan 29, 2013·Nucleic Acids Research·Clayton K CollingsJohn N Anderson
Feb 22, 2013·The Journal of Clinical Investigation·Sichuan XiDavid S Schrump
Mar 7, 2013·Nature Structural & Molecular Biology·Kevin Struhl, Eran Segal
Mar 8, 2013·PLoS Genetics·Gabriel E ZentnerSteven Henikoff
Sep 21, 2013·G3 : Genes - Genomes - Genetics·Yun ZhuLuay Nakhleh
Jun 25, 2013·Molecular Biology and Evolution·Bernhard SchaefkeWen-Hsiung Li
Dec 22, 2012·BMC Genomics·Zing Tsung-Yeh TsaiDaryi Wang
Nov 22, 2011·Nucleic Acids Research·Carl G de Boer, Timothy R Hughes
Dec 18, 2012·Nucleic Acids Research·Elizabeth D Howe, Jun S Song
Sep 29, 2012·Genome Biology·Vijender Singh, Tom Owen-Hughes
May 8, 2013·Genome Biology and Evolution·Zhenguo LinWen-Hsiung Li
May 24, 2013·Genome Biology and Evolution·Luke M Noble, Alex Andrianopoulos
May 4, 2012·Chromosoma·Steven Henikoff, Takehito Furuyama
Feb 20, 2016·Nucleic Acids Research·Hu JinJun S Song
Mar 17, 2012·Trends in Cell Biology·Vishwanath R Iyer

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Datasets Mentioned

BETA
GSE21960

Methods Mentioned

BETA
nucleosome sequencing
Illumina sequencing
PCR
feature extraction

Software Mentioned

LOWESS
Nuc
BLAT
eArray
Agilent
BioCyc
TestMOTIF

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