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Natural variation of histone modification and its impact on gene expression in the rat genome

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Item Type:Article
Title:Natural variation of histone modification and its impact on gene expression in the rat genome
Creators Name:Rintisch, C. and Heinig, M. and Bauerfeind, A. and Schafer, S. and Mieth, C. and Patone, G. and Hummel, O. and Chen, W. and Cook, S. and Cuppen, E. and Colome-Tatche, M. and Johannes, F. and Jansen, R.C. and Neil, H. and Werner, M. and Pravenec, M. and Vingron, M. and Hubner, N.
Abstract:Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships.
Keywords:Genetic Epigenesis, Genetic Promoter Regions, Genetic Transcription, Genetic Variation, Genome, Histones, Liver, Methylation, Myocardium, Post-Translational Protein Processing, Quantitative Trait Loci, Inbred Strains Rats, Transcription Factors, Animals, Rats
Source:Genome Research
ISSN:1088-9051
Publisher:Cold Spring Harbor Laboratory Press (U.S.A.)
Volume:24
Number:6
Page Range:942-953
Date:June 2014
Official Publication:https://doi.org/10.1101/gr.169029.113
PubMed:View item in PubMed

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