CLASH-Seq

CLASH-Seq

CLASH maps RNA-RNA interactions. In this method, RNA-protein complexes are UV-crosslinked and affinity-purified. RNA-RNA hybrids are ligated, isolated, and reverse-transcribed into cDNA. Deep sequencing of the cDNA provides high-resolution chimeric reads of RNA-RNA interactions.

Similar methods: miTRAP, SPLASH, hiCLIP, RAP, RPL

Pros:
  • Maps RNA-RNA interactions in vivo
  • Provides binding site–level resolution1
Cons:
  • Hybrid ligation may be difficult between short RNA fragments
  • Relatively low efficiency2
  • Requires known bait protein3