Global analysis of allele-specific expression in Arabidopsis thaliana

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dc.contributor.authorZhang, Xu
dc.contributor.authorBorevitz, Justin
dc.date.accessioned2015-12-13T22:48:42Z
dc.date.issued2009
dc.date.updated2016-02-24T09:42:25Z
dc.description.abstractGene expression is a complex trait determined by various genetic and nongenetic factors. Among the genetic factors, allelic difference may play a critical role in gene regulation. In this study we globally dissected cis (allelic) and trans sources of genetic variation in F1 hybrids between two Arabidopsis thaliana wild accessions, Columbia (Col) and Vancouver (Van), using a new high-density SNP-tiling array. This array tiles the whole genome with 35-bp resolution and interrogates 250,000 SNPs identified from resequencing of 20 diverse A. thaliana strains. Quantitative assessment of 12,311 genes identified 3811 genes differentially expressed between parents, 1665 genes with allele-specific expression, and 1688 genes controlled by composite trans-regulatory variation. Loci with cis- or trans-regulatory variation were mapped onto sequence polymorphisms, epigenetic modifications, and transcriptional specificity. Genes regulated in cis tend to be located in polymorphic chromosomal regions, are preferentially associated with repressive epigenetic marks, and exhibit high tissue expression specificity. Genes that vary due to trans regulation reside in relatively conserved chromosome regions, show activating epigenetic marks and generally constitutive gene expression. Our findings demonstrate a method of global functional characterization of allele-specific expression and highlight that chromatin structure is intertwined with evolution of cis- and trans-regulatory variation.
dc.identifier.issn0016-6731
dc.identifier.urihttp://hdl.handle.net/1885/80200
dc.publisherGenetics Society of America
dc.sourceGenetics (Print) ceased Dec 2009 - don't use
dc.subjectKeywords: cis acting element; trans acting factor; allele; Arabidopsis; article; chromatin structure; chromosome NOR; controlled study; DNA modification; epigenetics; gene control; gene expression; gene locus; gene mapping; gene sequence; genetic analysis; genetic
dc.titleGlobal analysis of allele-specific expression in Arabidopsis thaliana
dc.typeJournal article
local.bibliographicCitation.issue4
local.bibliographicCitation.lastpage954
local.bibliographicCitation.startpage943
local.contributor.affiliationZhang, Xu, University of Chicago
local.contributor.affiliationBorevitz, Justin, College of Medicine, Biology and Environment, ANU
local.contributor.authoremailu5083581@anu.edu.au
local.contributor.authoruidBorevitz, Justin, u5083581
local.description.embargo2037-12-31
local.description.notesImported from ARIES
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
local.identifier.ariespublicationf5625xPUB8497
local.identifier.citationvolume182
local.identifier.doi10.1534/genetics.109.103499
local.identifier.scopusID2-s2.0-70350142925
local.identifier.thomsonID000270214000003
local.identifier.uidSubmittedByf5625
local.type.statusPublished Version

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