MicroRNA target site identification by integrating sequence and binding information

Nat Methods. 2013 Jul;10(7):630-3. doi: 10.1038/nmeth.2489. Epub 2013 May 26.

Abstract

High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute proteins can pinpoint a microRNA (miRNA) target site within tens of bases but leaves the identity of the miRNA unresolved. A flexible computational framework, microMUMMIE, integrates sequence with cross-linking features and reliably identifies the miRNA family involved in each binding event. It considerably outperforms sequence-only approaches and quantifies the prevalence of noncanonical binding modes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Protein Interaction Mapping / methods*
  • RNA / genetics*
  • RNA / metabolism*
  • RNA-Binding Proteins / genetics*
  • Sequence Analysis, RNA / methods*
  • Systems Integration

Substances

  • RNA-Binding Proteins
  • RNA

Associated data

  • GEO/GSE41437
  • GEO/GSE46611