title: Genetic control of primary microRNA insight into cis- and trans-regulatory variations by RNA-seq.
abstract: To search for genetic regulators influencing miRNA transcript abundance, we performed a genome-wide association study (GWAS) to identify quantitative trait loci associated with primary miRNA transcript abundance (pri-miQTL) using genotype data from HapMap CEU phased data. We detected robust expression for 150 pri-miRNAs out of 1523 interrogated using RNA-seq. We have identified some pri-miRNAs that showed significant evidence for cis- (34%) and trans-pri-miQTLs (3%). Furthermore, we observed that multiple cis-pri-miQTLs, showed allele-specific expression associated with single pri-miRNA expression. Interestingly, a cis-regulatory variation influenced the expression levels of two pri-miRNAs that expressed identical mature sequences. We also observed that a single trans-regulatory variation was associated with multiple unrelated pri-miRNAs: rs292253 was associated with the expression of hsa-mir-3181, hsa-mir-3665 and hsa-mir-762. These findings revealed that the expression of pri-miRNA detected by RNA-seq can be used to identify pri-miQTLs, as an alternative method to dissect the genetic control mechanisms governing pri-miRNA expression.
authors.affiliation: Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Zhang
authors.forename: Liangde
authors.initials: L
authors.lastname: Xu
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.forename: Hongzhi
authors.initials: H
authors.lastname: Wang
authors.forename: Binsheng
authors.initials: B
authors.lastname: Gong
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.forename: Yadong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D045744:Cell Line, Tumor; D055106:Genome-Wide Association Study; D060148:HapMap Project; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs