title: RIP-Seq data analysis to determine RNA-protein associations.
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.
authors.affiliation: Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy.
authors.forename: Federico
authors.initials: F
authors.lastname: Zambelli
authors.forename: Giulio
authors.initials: G
authors.lastname: Pavesi
mesh_terms: D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011485:Protein Binding; D012313:RNA / Q000235:genetics / Q000378:metabolism*
chemical_list: D012313:RNA