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MicroRNA targeting specificity in mammals: determinants beyond seed pairing

ABSTRACT: This series consists of samples taken from HeLa transfected with miRNA duplexes. Keywords: other

ORGANISM(S): Homo sapiens

PROVIDER: GSE8501 | GEO | 2007/07/18

SECONDARY ACCESSION(S): PRJNA101607

REPOSITORIES: GEO

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MicroRNA targeting specificity in mammals: determinants beyond seed pairing.

Project description:Mammalian microRNAs (miRNAs) pair to 3'UTRs of mRNAs to direct their posttranscriptional repression. Important for target recognition are approximately 7 nt sites that match the seed region of the miRNA. However, these seed matches are not always sufficient for repression, indicating that other characteristics help specify targeting. By combining computational and experimental approaches, we uncovered five general features of site context that boost site efficacy: AU-rich nucleotide composition near the site, proximity to sites for coexpressed miRNAs (which leads to cooperative action), proximity to residues pairing to miRNA nucleotides 13-16, positioning within the 3'UTR at least 15 nt from the stop codon, and positioning away from the center of long UTRs. A model combining these context determinants quantitatively predicts site performance both for exogenously added miRNAs and for endogenous miRNA-message interactions. Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets.

| S-EPMC3800283 | biostudies-literature

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Project description:This series consists of samples taken from HeLa cells transfected with one of 7 (wild-type or mutant) miRNA duplexes and harvested either 12 or 24 hours later. Submitted for Nature publication Lim et al. Keywords = microRNA Keywords: other

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