Identification of RNA helicase target sites by UV cross-linking and analysis of cDNA

Markus T Bohnsack, David Tollervey, Sander Granneman

Research output: Contribution to journalArticlepeer-review


Many RNA helicases have been implicated in one or more pathways of RNA metabolism, but only in a very few cases have their target sites on the RNA been identified. Here, we give a detailed description of the UV cross-linking and analysis of cDNA (CRAC) method, and its application to the identification of binding sites of RNA-interacting helicases. CRAC makes use of a bipartite tag on the protein of interest and includes a purification step under highly denaturing conditions. This is particularly important for the accurate mapping of binding sites within large RNA-protein complexes-such as spliceosomes or preribosomes. Partial RNase digestion leaves a footprint of the protein covering the interaction site, and the UV cross-linking sites are frequently highlighted by microdeletions in cDNA sequence reads. Deep sequencing of cDNA libraries generated from cross-linked RNA fragments allows a genome-wide analysis of the interactome of RNA-binding proteins. In the case of RNA helicases, this has proven to be an important step toward their functional analysis.
Original languageEnglish
Pages (from-to)275-88
Number of pages14
JournalMethods in enzymology
Publication statusPublished - 16 Jun 2012


  • helicase
  • cross linking
  • RNA binding protein
  • CRAC


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