Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions

Adv Exp Med Biol. 2016:907:1-28. doi: 10.1007/978-3-319-29073-7_1.

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.

Keywords: BRIC_seq; CLIP-seq; HITS-CLIP; Microarray; PAR-CLIP; RNA processing; RNA-binding protein; RNA-seq; Ribo-seq; eCLIP; iCLIP.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Computational Biology / methods*
  • Datasets as Topic
  • Gene Expression Profiling / methods
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Immunoprecipitation
  • Models, Molecular
  • Mutation
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation
  • RNA / metabolism*
  • RNA Precursors / metabolism
  • RNA Processing, Post-Transcriptional
  • RNA Splicing
  • RNA Stability
  • RNA-Binding Motifs
  • RNA-Binding Proteins / metabolism*
  • Sequence Analysis, RNA

Substances

  • RNA Precursors
  • RNA-Binding Proteins
  • RNA