Spatial preferences of microRNA targets in 3' untranslated regions.

Published online

Journal Article

BACKGROUND: MicroRNAs are an important class of regulatory RNAs which repress animal genes by preferentially interacting with complementary sequence motifs in the 3' untranslated region (UTR) of target mRNAs. Computational methods have been developed which can successfully predict which microRNA may target which mRNA on a genome-wide scale. RESULTS: We address how predicted target sites may be affected by alternative polyadenylation events changing the 3'UTR sequence. We find that two thirds of targeted genes have alternative 3'UTRs, with 40% of predicted target sites located in alternative UTR segments. We propose three classes based on whether the target sites fall within constitutive and/or alternative UTR segments, and examine the spatial distribution of predicted targets in alternative UTRs. In particular, there is a strong preference for targets to be located in close vicinity of the stop codon and the polyadenylation sites. CONCLUSION: The transcript diversity seen in non-coding regions, as well as the relative location of miRNA target sites defined by it, has a potentially large impact on gene regulation by miRNAs and should be taken into account when defining, predicting or validating miRNA targets.

Full Text

Duke Authors

Cited Authors

  • Majoros, WH; Ohler, U

Published Date

  • June 7, 2007

Published In

Volume / Issue

  • 8 /

Start / End Page

  • 152 -

PubMed ID

  • 17555584

Pubmed Central ID

  • 17555584

Electronic International Standard Serial Number (EISSN)

  • 1471-2164

Digital Object Identifier (DOI)

  • 10.1186/1471-2164-8-152

Language

  • eng

Conference Location

  • England