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| Item Type: | Article |
|---|---|
| Title: | High-resolution profiling of protein occupancy on polyadenylated RNA transcripts |
| Creators Name: | Munschauer, M., Schueler, M., Dieterich, C. and Landthaler, M. |
| Abstract: | A key prerequisite to understand how gene regulatory processes are controlled by the interplay of RNA-binding proteins (RBPs) and ribonucleoprotein complexes with RNAs is the generation of comprehensive high-resolution maps of protein-RNA interactions. Recent advances in next-generation sequencing technology accelerated the development of various crosslinking and immunoprecipitation (CLIP) approaches to broadly identify RNA regions contacted by RNA-binding proteins. However these methods only consider single RNA-binding proteins and their contact sites, irrespective of the overall cis-regulatory sequence space contacted by other RNA interacting factors. Here we describe the application of protein occupancy profiling, a novel approach that globally displays the RNA contact sites of the poly(A)+ RNA-bound proteome. Protein occupancy profiling enables the generation of transcriptome-wide maps of protein-RNA interactions on polyadenylated transcripts and narrows the sequence search space for transcript regions involved in cis-regulation of gene expression in response to internal or external stimuli, altered cellular programs or disease. |
| Keywords: | CLIP, PAR-CLIP, mRNA, lincRNA, Protein Occupancy Profiling, Non-Coding RNA, Protein-RNA Interaction, RNA-Binding Protein, Next-Generation Sequencing, Animals, Mice |
| Source: | Methods |
| ISSN: | 1046-2023 |
| Publisher: | Elsevier / Academic Press |
| Volume: | 65 |
| Number: | 3 |
| Page Range: | 302-309 |
| Date: | February 2014 |
| Official Publication: | https://doi.org/10.1016/j.ymeth.2013.09.017 |
| PubMed: | View item in PubMed |
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