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Nature Research, Nature Methods, 7(10), p. 630-633, 2013

DOI: 10.1038/nmeth.2489

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MicroRNA Target Site Identification by Integrating Sequence and Binding Information

Journal article published in 2013 by William H. Majoros, Parawee Lekprasert, Neelanjan Mukherjee, Rebecca L. Skalsky, David L. Corcoran ORCID, Bryan R. Cullen, Uwe Ohler
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.