Open AccessExon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation
Author(s) -
Guan Leying,
Yang Qian,
Gu Mengting,
Chen Liang,
Zhang Xuegong
Publication year - 2014
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-014-0031-9
Subject(s) - exon , expression quantitative trait loci , biology , alternative splicing , rna splicing , genetics , quantitative trait locus , gene , international hapmap project , regulation of gene expression , gene expression , computational biology , rna , genome , single nucleotide polymorphism , human genome , genotype
Alternative splicing is a ubiquitous mechanism of post‐transcriptional regulation of gene expression and produces multiple isoforms from the same genes. Expression quantitative trait loci (eQTL) has been a major method for finding associations between gene expression and genomic variations. Differences in alternative splicing isoforms are resulted from differences in the expression of exons. We propose to use exon expression QTL (eeQTL) to study the genomic variations that are associated with splicing regulation. A stringent criterion was adopted to study gene‐level eQTLs and exon‐level eeQTLs for both cis ‐ and trans ‐ factors. From experiments on an RNA‐sequencing (RNA‐Seq) data set of HapMap samples, we observed that compared with eQTLs, more eeQTL trans ‐factors can be found than cis ‐factors, and many of the eeQTLs cannot be found at the gene level. This work highlights that the regulation of exons adds another layer of regulation on gene expression, and that eeQTL analysis is a new approach for investigating genome‐wide genomic variations that are involved in the regulation of alternative splicing.