Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region

Wanjun Gu, Xiaofei Wang, Chuanying Zhai, Tong Zhou, Xueying Xie

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Recent analyses have revealed many functional microRNA (miRNA) targets in mammalian protein coding regions. But, the mechanisms that ensure miRNA function when their target sites are located in protein coding regions of mammalian mRNA transcripts are largely unknown. In this paper, we investigate some potential biological factors, such as target site accessibility and local translation efficiency. We computationally analyze these two factors using experimentally identified miRNA targets in human protein coding region. We find site accessibility is significantly increased in miRNA target region to facilitate miRNA binding. At the mean time, local translation efficiency is also selectively decreased near miRNA target region. GC-poor codons are preferred in the flank region of miRNA target sites to ease the access of miRNA targets. Within-genome analysis shows substantial variations of site accessibility and local translation efficiency among different miRNA targets in the genome. Further analyses suggest target gene's GC content and conservation level could explain some of the differences in site accessibility. On the other hand, target gene's functional importance and conservation level can affect local translation efficiency near miRNA target region. We hence propose both site accessibility and local translation efficiency are important in miRNA action when miRNA target sites are located in mammalian protein coding regions.

Original languageEnglish (US)
Article numbere63403
JournalPLoS One
Volume8
Issue number5
DOIs
StatePublished - May 6 2013
Externally publishedYes

Fingerprint

MicroRNAs
microRNA
Open Reading Frames
open reading frames
Proteins
translation (genetics)
Genes
Conservation
Genome
genome
Base Composition
Biological Factors
codons
Codon
Statistical Factor Analysis
genes
Messenger RNA

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region. / Gu, Wanjun; Wang, Xiaofei; Zhai, Chuanying; Zhou, Tong; Xie, Xueying.

In: PLoS One, Vol. 8, No. 5, e63403, 06.05.2013.

Research output: Contribution to journalArticle

Gu, Wanjun ; Wang, Xiaofei ; Zhai, Chuanying ; Zhou, Tong ; Xie, Xueying. / Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region. In: PLoS One. 2013 ; Vol. 8, No. 5.
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