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Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences.

Abstract：

:MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming precursors that play a crucial role as post-transcriptional regulators in eukaryotes and viruses. In the past years, many microRNA target genes (MTGs) have been identified experimentally. However, because of the high costs of experimental approaches, target genes databases remain incomplete. Although several target prediction programs have been developed in the recent years to identify MTGs in silico, their specificity and sensitivity remain low. Here, we propose a new approach called MirAncesTar, which uses ancestral genome reconstruction to boost the accuracy of existing MTGs prediction tools for human miRNAs. For each miRNA and each putative human target UTR, our algorithm makes uses of existing prediction tools to identify putative target sites in the human UTR, as well as in its mammalian orthologs and inferred ancestral sequences. It then evaluates evidence in support of selective pressure to maintain target site counts (rather than sequences), accounting for the possibility of target site turnover. It finally integrates this measure with several simpler ones using a logistic regression predictor. MirAncesTar improves the accuracy of existing MTG predictors by 26% to 157%. Source code and prediction results for human miRNAs, as well as supporting evolutionary data are available at http://cs.mcgill.ca/∼blanchem/mirancestar.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Leclercq M,Diallo AB,Blanchette M

doi

10.1093/nar/gkw1085

subject

Has Abstract

pub_date

2017-01-25 00:00:00

pages

556-566

issue

2

eissn

0305-1048

issn

1362-4962

pii

gkw1085

journal_volume

45

pub_type

杂志文章

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