Feb 7, 2012

DNase I sensitivity QTLs are a major determinant of human expression variation

Nature
Jacob F DegnerJonathan K Pritchard

Abstract

The mapping of expression quantitative trait loci (eQTLs) has emerged as an important tool for linking genetic variation to changes in gene regulation. However, it remains difficult to identify the causal variants underlying eQTLs, and little is known about the regulatory mechanisms by which they act. Here we show that genetic variants that modify chromatin accessibility and transcription factor binding are a major mechanism through which genetic variation leads to gene expression differences among humans. We used DNase I sequencing to measure chromatin accessibility in 70 Yoruba lymphoblastoid cell lines, for which genome-wide genotypes and estimates of gene expression levels are also available. We obtained a total of 2.7 billion uniquely mapped DNase I-sequencing (DNase-seq) reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 8,902 locations at which the DNase-seq read depth correlated significantly with genotype at a nearby single nucleotide polymorphism or insertion/deletion (false discovery rate = 10%). We call such variants 'DNase I sensitivity quantitative trait loci' (dsQTLs). We found that dsQTLs are strongly enriched within inferred transcription factor bin...Continue Reading

Mentioned in this Paper

Quantitative Trait Loci
Deoxyribonuclease I
Gene Deletion Abnormality
DNA Footprinting
Gene Expression
Sequencing
Deletion Mutation
Transcription Factor Binding
Sequence Determinations, DNA
DNASE1

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