CLASH-Seq
CLASH-Seq
Crosslinking, ligation, and sequencing of hybrids (CLASH-Seq) maps RNA-RNA interactions. In this method RNA-protein complexes are UV crosslinked and affinity-purified. RNA-RNA hybrids are then ligated, isolated, and reverse-transcribed to cDNA. Deep sequencing of the cDNA provides high-resolution chimeric reads of RNA-RNA interactions.
Pros:
- Maps RNA-RNA interactions
- Performed in vivo
Cons:
- Hybrid ligation may be difficult between short RNA fragments