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Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

ABSTRACT: It is known that genetic variants can affect gene expression, but it is not yet completely clear through what mechanisms genetic variation mediate this expression. We therefore compared the cis-effect of single nucleotide polymorphisms (SNPs) on gene expression between blood samples from 1,240 human subjects and four primary non-blood tissues (liver, subcutaneous, and visceral adipose tissue and skeletal muscle) from 85 subjects. We characterized four different mechanisms for 2,072 probes that show tissue-dependent genetic regulation between blood and non-blood tissues: on average 33.2% only showed cis-regulation in non-blood tissues; 14.5% of the eQTL probes were regulated by different, independent SNPs depending on the tissue of investigation. 47.9% showed a different effect size although they were regulated by the same SNPs. Surprisingly, we observed that 4.4% were regulated by the same SNP but with opposite allelic direction. We show here that SNPs that are located in transcriptional regulatory elements are enriched for tissue-dependent regulation, including SNPs at 3' and 5' untranslated regions (P?=?1.84×10(-5) and 4.7×10(-4), respectively) and SNPs that are synonymous-coding (P?=?9.9×10(-4)). SNPs that are associated with complex traits more often exert a tissue-dependent effect on gene expression (P?=?2.6×10(-10)). Our study yields new insights into the genetic basis of tissue-dependent expression and suggests that complex trait associated genetic variants have even more complex regulatory effects than previously anticipated.

SUBMITTER: Fu J

PROVIDER: S-EPMC3261927 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

Fu Jingyuan J Wolfs Marcel G M MG Deelen Patrick P Westra Harm-Jan HJ Fehrmann Rudolf S N RS Te Meerman Gerard J GJ Buurman Wim A WA Rensen Sander S M SS Groen Harry J M HJ Weersma Rinse K RK van den Berg Leonard H LH Veldink Jan J Ophoff Roel A RA Snieder Harold H van Heel David D Jansen Ritsert C RC Hofker Marten H MH Wijmenga Cisca C Franke Lude L

PLoS genetics 20120119 1

It is known that genetic variants can affect gene expression, but it is not yet completely clear through what mechanisms genetic variation mediate this expression. We therefore compared the cis-effect of single nucleotide polymorphisms (SNPs) on gene expression between blood samples from 1,240 human subjects and four primary non-blood tissues (liver, subcutaneous, and visceral adipose tissue and skeletal muscle) from 85 subjects. We characterized four different mechanisms for 2,072 probes that s ...[more]

PMID: 22275870

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Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

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Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

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