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Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing

Item Type:Review
Title:Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing
Creators Name:Milek, M. and Wyler, E. and Landthaler, M.
Abstract:Protein-RNA interactions are emerging as an important functional element in the regulation of gene expression. Cross-linking of proteins to RNA by UV irradiation followed by immunoprecipitation (CLIP) has provided a crucial tool for research in this field. Initially, the bottleneck of the method was the relatively low number of identified RNA binding sites. It was only the arrival of next-generation sequencing that allowed a comprehensive and unbiased description of the cross-linked protein-RNA fragments. Here, we summarize recent progress in the study of protein-RNA interactions, as well as some of the important findings obtained using different CLIP approaches in cultured cells and organisms. These efforts allowed the identification of functional RNA-binding sites for a wide range of RNA-interacting proteins. Experimental and bioinformatic progress will further advance this dynamic area of research. The combination of high-resolution protein-RNA interaction maps with transcriptome-wide data describing the stability, modifications and structures of RNAs, in addition to protein expression profiling, will provide deeper insight into post-transcriptional and translational regulatory events and mechanisms.
Keywords:Post-Transcriptional Regulation, Protein-RNA Interactions, Cross-Linking and Immunoprecipitation, CLIP, Next-Generation Sequencing, Animals
Source:Seminars in Cell & Developmental Biology
ISSN:1084-9521
Publisher:Academic Press / Elsevier (U.K.)
Volume:23
Number:2
Page Range:206-212
Date:April 2012
Official Publication:https://doi.org/10.1016/j.semcdb.2011.12.001
PubMed:View item in PubMed

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