Jan 24, 2013

Human disease-associated genetic variation impacts large intergenic non-coding RNA expression

PLoS Genetics
Vinod KumarCisca Wijmenga

Abstract

Recently it has become clear that only a small percentage (7%) of disease-associated single nucleotide polymorphisms (SNPs) are located in protein-coding regions, while the remaining 93% are located in gene regulatory regions or in intergenic regions. Thus, the understanding of how genetic variations control the expression of non-coding RNAs (in a tissue-dependent manner) has far-reaching implications. We tested the association of SNPs with expression levels (eQTLs) of large intergenic non-coding RNAs (lincRNAs), using genome-wide gene expression and genotype data from five different tissues. We identified 112 cis-regulated lincRNAs, of which 45% could be replicated in an independent dataset. We observed that 75% of the SNPs affecting lincRNA expression (lincRNA cis-eQTLs) were specific to lincRNA alone and did not affect the expression of neighboring protein-coding genes. We show that this specific genotype-lincRNA expression correlation is tissue-dependent and that many of these lincRNA cis-eQTL SNPs are also associated with complex traits and diseases.

  • References37
  • Citations148

Mentioned in this Paper

Establishment and Maintenance of Localization
Genome-Wide Association Study
Diabetes Mellitus, Non-Insulin-Dependent
Quantitative Trait Loci
CDKN2B-AS1 gene
Exons
Genome
RNA, Untranslated
Peripheral Blood
Transcription, Genetic

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