Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

Mapping of expression quantitative trait loci (eQTLs) is an important technique for studying how genetic variation affects gene regulation in natural populations. In a previous study using Illumina expression data from human lymphoblastoid cell lines, we reported that cis-eQTLs are especially enrich...

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Autores principales:	Jean-Baptiste Veyrieras, Daniel J Gaffney, Joseph K Pickrell, Yoav Gilad, Matthew Stephens, Jonathan K Pritchard
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d400baa427bf478d840b8ba754701f57
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spelling	oai:doaj.org-article:d400baa427bf478d840b8ba754701f572021-11-18T07:28:04ZExon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.1932-620310.1371/journal.pone.0030629https://doaj.org/article/d400baa427bf478d840b8ba754701f572012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22359548/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Mapping of expression quantitative trait loci (eQTLs) is an important technique for studying how genetic variation affects gene regulation in natural populations. In a previous study using Illumina expression data from human lymphoblastoid cell lines, we reported that cis-eQTLs are especially enriched around transcription start sites (TSSs) and immediately upstream of transcription end sites (TESs). In this paper, we revisit the distribution of eQTLs using additional data from Affymetrix exon arrays and from RNA sequencing. We confirm that most eQTLs lie close to the target genes; that transcribed regions are generally enriched for eQTLs; that eQTLs are more abundant in exons than introns; and that the peak density of eQTLs occurs at the TSS. However, we find that the intriguing TES peak is greatly reduced or absent in the Affymetrix and RNA-seq data. Instead our data suggest that the TES peak observed in the Illumina data is mainly due to exon-specific QTLs that affect 3' untranslated regions, where most of the Illumina probes are positioned. Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation.Jean-Baptiste VeyrierasDaniel J GaffneyJoseph K PickrellYoav GiladMatthew StephensJonathan K PritchardPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e30629 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jean-Baptiste Veyrieras Daniel J Gaffney Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
description	Mapping of expression quantitative trait loci (eQTLs) is an important technique for studying how genetic variation affects gene regulation in natural populations. In a previous study using Illumina expression data from human lymphoblastoid cell lines, we reported that cis-eQTLs are especially enriched around transcription start sites (TSSs) and immediately upstream of transcription end sites (TESs). In this paper, we revisit the distribution of eQTLs using additional data from Affymetrix exon arrays and from RNA sequencing. We confirm that most eQTLs lie close to the target genes; that transcribed regions are generally enriched for eQTLs; that eQTLs are more abundant in exons than introns; and that the peak density of eQTLs occurs at the TSS. However, we find that the intriguing TES peak is greatly reduced or absent in the Affymetrix and RNA-seq data. Instead our data suggest that the TES peak observed in the Illumina data is mainly due to exon-specific QTLs that affect 3' untranslated regions, where most of the Illumina probes are positioned. Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation.
format	article
author	Jean-Baptiste Veyrieras Daniel J Gaffney Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard
author_facet	Jean-Baptiste Veyrieras Daniel J Gaffney Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard
author_sort	Jean-Baptiste Veyrieras
title	Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
title_short	Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
title_full	Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
title_fullStr	Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
title_full_unstemmed	Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
title_sort	exon-specific qtls skew the inferred distribution of expression qtls detected using gene expression array data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/d400baa427bf478d840b8ba754701f57
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Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

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