High-throughput characterization of protein-RNA interactions

Briefings in Functional Genomics
Kate B CookQuaid D Morris

Abstract

RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA-protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA-protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.

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Methods Mentioned

BETA
footprinting
RIP-chip
SELEX
immunoprecipitation
PAR-CLIP
CLIP-seq
PCR
Illumina sequencing
RIP
CLIP

Related Concepts

DNA Conformation
Plasma Protein Binding Capacity
RNA
RNA-Binding Proteins
High-Throughput Chemical Assays
Genome
RNA, Viral
Structure
Determination Aspects
RNA Binding

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