MicroRNA target site identification by integrating sequence and binding information

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

doi:10.1038/nmeth.2489

MicroRNA target site identification by integrating sequence and binding information

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

Research output: Contribution to journal › Article › peer-review

46 Scopus citations

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 language	English (US)
Pages (from-to)	630-633
Number of pages	4
Journal	Nature Methods
Volume	10
Issue number	7
DOIs	https://doi.org/10.1038/nmeth.2489
State	Published - Jul 2013
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.2489

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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.",

author = "Majoros, {William H.} and Parawee Lekprasert and Neelanjan Mukherjee and Skalsky, {Rebecca L.} and Corcoran, {David L.} and Cullen, {Bryan R.} and Uwe Ohler",

note = "Funding Information: This work was supported by grants from the US National Science Foundation (MCB-0822033) and US National Institutes of Health (NIH R01-GM104962) to U.O. and by awards from the NIH (R01-AI067968; R01-DA030086) to B.R.C. Contributions by R.L.S. were additionally supported by a Duke Center for AIDS Research small grant award (P30-AI064518). We thank S. Grosswendt and M. Piechotta for critical reading of a manuscript draft.",

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AU - Majoros, William H.

AU - Lekprasert, Parawee

AU - Mukherjee, Neelanjan

AU - Skalsky, Rebecca L.

AU - Corcoran, David L.

AU - Cullen, Bryan R.

AU - Ohler, Uwe

N1 - Funding Information: This work was supported by grants from the US National Science Foundation (MCB-0822033) and US National Institutes of Health (NIH R01-GM104962) to U.O. and by awards from the NIH (R01-AI067968; R01-DA030086) to B.R.C. Contributions by R.L.S. were additionally supported by a Duke Center for AIDS Research small grant award (P30-AI064518). We thank S. Grosswendt and M. Piechotta for critical reading of a manuscript draft.

PY - 2013/7

Y1 - 2013/7

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MicroRNA target site identification by integrating sequence and binding information

Abstract

ASJC Scopus subject areas

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