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.

SUBMITTER: Majoros WH 

PROVIDER: S-EPMC3818907 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature