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MicroRNA target site identification by integrating sequence and binding information
W. Majoros,
P. Lekprasert,
Neelanjan Mukherjee,
R. Skalsky,
D. Corcoran,
B. Cullen,
Uwe Ohler
Nat. Methods
2013
10 7 630--633
PubMed Central
DOI
PubMed
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.
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