MicroRNA target site identification by integrating sequence and binding information

William H. Majoros, Parawee Lekprasert, Neelanjan Mukherjee, Rebecca Skalsky, David L. Corcoran, Bryan R. Cullen, Uwe Ohler

Research output: Contribution to journalArticle

37 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)630-633
Number of pages4
JournalNature Methods
Volume10
Issue number7
DOIs
StatePublished - 2013
Externally publishedYes

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MicroRNAs
Argonaute Proteins
Immunoprecipitation
Throughput
RNA

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Majoros, W. H., Lekprasert, P., Mukherjee, N., Skalsky, R., Corcoran, D. L., Cullen, B. R., & Ohler, U. (2013). MicroRNA target site identification by integrating sequence and binding information. Nature Methods, 10(7), 630-633. https://doi.org/10.1038/nmeth.2489

MicroRNA target site identification by integrating sequence and binding information. / Majoros, William H.; Lekprasert, Parawee; Mukherjee, Neelanjan; Skalsky, Rebecca; Corcoran, David L.; Cullen, Bryan R.; Ohler, Uwe.

In: Nature Methods, Vol. 10, No. 7, 2013, p. 630-633.

Research output: Contribution to journalArticle

Majoros, WH, Lekprasert, P, Mukherjee, N, Skalsky, R, Corcoran, DL, Cullen, BR & Ohler, U 2013, 'MicroRNA target site identification by integrating sequence and binding information', Nature Methods, vol. 10, no. 7, pp. 630-633. https://doi.org/10.1038/nmeth.2489
Majoros, William H. ; Lekprasert, Parawee ; Mukherjee, Neelanjan ; Skalsky, Rebecca ; Corcoran, David L. ; Cullen, Bryan R. ; Ohler, Uwe. / MicroRNA target site identification by integrating sequence and binding information. In: Nature Methods. 2013 ; Vol. 10, No. 7. pp. 630-633.
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