H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast

BMC Genomics
Muxin GuCatherine B Millar

Abstract

The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in budding yeast, where it co-localises with histone marks associated with active promoters. By comparing H2A.Z binding to global gene expression in budding yeast strains engineered so that normally unstable transcripts are abundant, we show that H2A.Z is required for normal levels of antisense transcripts as well as sense ones. High levels of H2A.Z at antisense promoters are associated with decreased antisense transcript levels when H2A.Z is deleted, indicating that H2A.Z has an activating effect on antisense transcripts. Decreases in antisense transcripts affected by H2A.Z are accompanied by increased levels of paired sense transcripts. The effect of H2A.Z on protein coding gene expression is a reflection of its importance for normal levels of both sense and antisense transcripts.

References

Aug 1, 1996·Molecular and Cellular Biology·X Liu GorovskyMA
Aug 23, 2001·Current Biology : CB·R FaastI Lyons
Aug 10, 2004·The Journal of Biological Chemistry·Patricia RidgwayDavid J Tremethick
Aug 27, 2005·PLoS Biology·Chih Long LiuOliver J Rando
Dec 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Bing LiJerry L Workman
Mar 18, 2006·Genes & Development·Catherine B MillarMichael Grunstein
Oct 3, 2006·PLoS Genetics·Dustin L Updike, Susan E Mango
Dec 14, 2007·Nature·Iestyn WhitehouseToshio Tsukiyama
Jan 27, 2009·Nature·Zhenyu XuLars M Steinmetz
Feb 24, 2009·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Ryan Draker, Peter Cheung
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Dec 22, 2009·Cell Cycle·Amy SvotelisLuc Gaudreau
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Jan 21, 2011·Nature·L Stirling Churchman, Jonathan S Weissman
Apr 13, 2011·PLoS Genetics·Benoit GuillemetteRichard J Festenstein
Apr 23, 2011·Science·Nicholas RhindChad Nusbaum
Jul 21, 2011·Biochimie·Mathieu TisseurAntonin Morillon
Dec 29, 2011·Seminars in Cell & Developmental Biology·Sophie R AtkinsonJürg Bähler
Apr 12, 2012·The Journal of Biological Chemistry·Daniel WrattingCatherine B Millar
Jun 19, 2012·Molecular Microbiology·Michael E Donaldson, Barry J Saville
Oct 17, 2012·PLoS Genetics·Devin Coleman-Derr, Daniel Zilberman
Jan 11, 2013·The Biochemical Journal·Catherine B Millar
Jun 1, 2013·BMC Biology·Aleksandra E KornienkoFlorian M Pauler

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Citations

Apr 14, 2016·Trends in Genetics : TIG·Dia N Bagchi, Vishwanath R Iyer
Dec 6, 2017·Genes & Development·Yoo Jin JooStephen Buratowski
May 4, 2017·Proceedings of the National Academy of Sciences of the United States of America·Corey M NemecAseem Z Ansari
Dec 28, 2016·Nucleic Acids Research·Eva KlopfChristoph Schüller
Apr 28, 2017·Genes & Development·Lauren T NevesTracy L Johnson
Aug 2, 2019·Nature Communications·Leandro QuadranaVincent Colot

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Methods Mentioned

BETA
ChIP-chip
ChIP-seq
ChIP
RNA-seq

Software Mentioned

DESeq2
Bowtie

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