title: MicroRNA targeting specificity in mammals: determinants beyond seed pairing.
abstract: 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.
authors.affiliation: Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Grimson
authors.forename: Kyle Kai-How
authors.initials: KK
authors.lastname: Farh
authors.forename: Wendy K
authors.initials: WK
authors.lastname: Johnston
authors.forename: Philip
authors.initials: P
authors.lastname: Garrett-Engele
authors.forename: Lee P
authors.initials: LP
authors.lastname: Lim
authors.forename: David P
authors.initials: DP
authors.lastname: Bartel
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites; D018388:Codon, Terminator / Q000235:genetics; D017124:Conserved Sequence; D015536:Down-Regulation / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D008322:Mammals / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D020413:3' Untranslated Regions; D018388:Codon, Terminator; D035683:MicroRNAs; D009711:Nucleotides; D012333:RNA, Messenger