title: Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.
abstract: After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. The recent explosion in genomics techniques has enabled transcriptome-wide profiling of RNA processing in an unbiased manner. However, it has also brought with it both experimental challenges in developing improved methods to probe distinct processing steps, as well as computational challenges in data storage, processing, and analysis tools to enable large-scale interpretation in the genomics era. In this chapter we review experimental techniques and challenges in profiling various aspects of RNA processing, as well as recent efforts to develop analyses integrating multiple data sources and techniques to infer RNA regulatory networks.
authors.affiliation: Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, CA, USA.
authors.forename: Eric L
authors.initials: EL
authors.lastname: Van Nostrand
authors.affiliation: Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, CA, USA.
authors.forename: Stephanie C
authors.initials: SC
authors.lastname: Huelga
authors.affiliation: Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, CA, USA. geneyeo@ucsd.edu.|Molecular Engineering Laboratory, A*STAR, Singapore, Singapore. geneyeo@ucsd.edu.|Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. geneyeo@ucsd.edu.
authors.forename: Gene W
authors.initials: GW
authors.lastname: Yeo
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D066264:Datasets as Topic; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D047468:Immunoprecipitation; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000378:metabolism*; D012322:RNA Precursors / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012326:RNA Splicing; D020871:RNA Stability; D000071376:RNA-Binding Motifs; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D012322:RNA Precursors; D016601:RNA-Binding Proteins; D012313:RNA
keywords: BRIC_seq; CLIP-seq; HITS-CLIP; Microarray; PAR-CLIP; RNA processing; RNA-binding protein; RNA-seq; Ribo-seq; eCLIP; iCLIP