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Semin Cell Dev Biol. 2012 Apr;23(2):206-12. doi: 10.1016/j.semcdb.2011.12.001. Epub 2011 Dec 27.

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

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  • 1Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany. miha.milek@mdc-berlin.de

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.

Copyright © 2011 Elsevier Ltd. All rights reserved.

PMID:
22212136
[PubMed - indexed for MEDLINE]
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