title: MicroRNA target site identification by integrating sequence and binding information.
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.
authors.affiliation: Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA.
authors.forename: William H
authors.initials: WH
authors.lastname: Majoros
authors.forename: Parawee
authors.initials: P
authors.lastname: Lekprasert
authors.forename: Neelanjan
authors.initials: N
authors.lastname: Mukherjee
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Skalsky
authors.forename: David L
authors.initials: DL
authors.lastname: Corcoran
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Cullen
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
mesh_terms: D000465:Algorithms; D025941:Protein Interaction Mapping / Q000379:methods*; D012313:RNA / Q000235:genetics* / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D018511:Systems Integration
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA