Next-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the identification of the RNAs bound by a given RBP.

RIP-Seq data analysis to determine RNA-protein associations / F. Zambelli, G. Pavesi (METHODS IN MOLECULAR BIOLOGY). - In: RNA bioinformatics / [a cura di] E. Picardi. - New York : Springer, 2015. - ISBN 9781493922901. - pp. 293-303 [10.1007/978-1-4939-2291-8_18]

RIP-Seq data analysis to determine RNA-protein associations

F. Zambelli
Primo
;
G. Pavesi
Ultimo
2015

Abstract

Next-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the identification of the RNAs bound by a given RBP.
CLIP-Seq; Immunoprecipitation; Next-generation sequencing; PAR-CLIP; RIP-Seq; RNA binding protein
Settore BIO/11 - Biologia Molecolare
Settore INF/01 - Informatica
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/261736
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