Combinatorial Cis-regulation in Saccharomyces Species

G3 : Genes - Genomes - Genetics
Aaron T Spivak, Gary D Stormo

Abstract

Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs) controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1) chromatin immunoprecipitation data for colocalization of transcription factors, (2) gene expression data for coexpression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF) occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyz...Continue Reading

References

Jul 1, 1991·Molecular and Cellular Biology·C DevlinK T Arndt
Jan 20, 1985·Journal of Molecular Biology·M A Shea, G K Ackers
Feb 12, 1999·Nucleic Acids Research·S MertinV R Harley
Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Aug 10, 2000·Cell·T R HughesS H Friend
Dec 5, 2000·Molecular Biology of the Cell·A P GaschP O Brown
Jun 21, 2001·Proceedings of the National Academy of Sciences of the United States of America·B RaughtN Sonenberg
Jul 13, 2001·Bioinformatics·D GuhaThakurta, G D Stormo
Jul 26, 2002·Nature·Guri GiaeverMark Johnston
Sep 28, 2002·Science·Michelle N ArbeitmanKevin P White
Nov 26, 2002·Molecular and Cellular Biology·Marilyn G Pray-GrantPatrick A Grant
Jun 6, 2003·Biochemical and Biophysical Research Communications·Mijin KimByeong Jae Lee
Nov 25, 2003·Nucleic Acids Research·Nilanjana Banerjee, Michael Q Zhang
Apr 8, 2004·Molecular Cell·Ronald A Butow, Narayan G Avadhani
Apr 16, 2004·Cell·Michael A Beer, Saeed Tavazoie
Aug 4, 2004·Genome Biology·Mamoru KatoMichael Q Zhang
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Nov 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Debopriya DasMichael Q Zhang
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
May 19, 2007·Nature Reviews. Genetics·Uri Alon
May 29, 2007·PLoS Computational Biology·Scott W Doniger, Justin C Fay
Nov 15, 2007·Nucleic Acids Research·Bobby-Joe BreitkreutzMike Tyers
Dec 7, 2007·Genome Biology·Zihua HuJames F Collins
Jan 17, 2008·Molecular Systems Biology·Itay TiroshNaama Barkai
Feb 29, 2008·PLoS Biology·Brian B TuchAlexander D Johnson

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Citations

Jun 12, 2016·Nucleic Acids Research·Matthias Siebert, Johannes Söding
Dec 20, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·A K M Firoj MahmudSoumyadeep Nandi

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Datasets Mentioned

BETA
GSE60281

Methods Mentioned

BETA
ChIP
ChIP-Seq
ChIP-chip
immunoprecipitation
Illumina sequencing
PCR
environmental stress

Software Mentioned

MACS

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