Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing.
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.
Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany. miha.milek@mdc-berlin.de
Miha
M
Milek
Emanuel
E
Wyler
Markus
M
Landthaler
D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D003432:Cross-Linking Reagents / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D025941:Protein Interaction Mapping; D012313:RNA / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic; D014466:Ultraviolet Rays
D003432:Cross-Linking Reagents; D016601:RNA-Binding Proteins; D012313:RNA