Format

Send to

Choose Destination
Methods Mol Biol. 2016;1358:153-73. doi: 10.1007/978-1-4939-3067-8_10.

PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

Author information

1
Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS / NIH, 50 South Drive, 20892, Bethesda, MD, USA.
2
Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS / NIH, 50 South Drive, 20892, Bethesda, MD, USA. markus.hafner@nih.gov.

Abstract

During post-transcriptional gene regulation (PTGR), RNA binding proteins (RBPs) interact with all classes of RNA to control RNA maturation, stability, transport, and translation. Here, we describe Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a transcriptome-scale method for identifying RBP binding sites on target RNAs with nucleotide-level resolution. This method is readily applicable to any protein directly contacting RNA, including RBPs that are predicted to bind in a sequence- or structure-dependent manner at discrete RNA recognition elements (RREs), and those that are thought to bind transiently, such as RNA polymerases or helicases.

KEYWORDS:

Binding site; Cross-linking and immunoprecipitation (CLIP); Noncoding RNA; Photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP); Posttranscriptional gene regulation (PTGR); RNA; RNA recognition element (RRE); RNA-binding protein (RBP); mRNA

PMID:
26463383
PMCID:
PMC5142217
DOI:
10.1007/978-1-4939-3067-8_10
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Springer Icon for PubMed Central
Loading ...
Support Center