Jan 4, 2012

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

Seminars in Cell & Developmental Biology
Miha MilekMarkus Landthaler

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.

  • References56
  • Citations38

References

Mentioned in this Paper

TARDBP gene
Metabolic Process, Cellular
Neuro-Oncological Ventral Antigen 2
NOVA1 protein, human
AGO2 gene
NOVA2 wt Allele
Covalent Interaction
Argonaute Proteins
RRP9 gene
Exons

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