CLASH
Crosslinking, Ligation, and Sequencing of Hybrids
CLASH maps RNA-RNA interactions (Kudla et al., 2011) (Helwak et al., 2013). 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
Advantages:
- Maps RNA-RNA interactions in vivo
- Provides binding site_level resolution (Imig et al., 2015)
Disadvantages:
- Hybrid ligation may be difficult between short RNA fragments
- Relatively low efficiency (Hausser et al., 2014)
- Requires known bait protein (Lu et al., 2016)
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Chou C. H., Chang N. W., Shrestha S., et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016;44:D239-247
Hausser J. and Zavolan M. Identification and consequences of miRNA-target interactions–beyond repression of gene expression. Nat Rev Genet. 2014;15:599-612
References:
Imig J., Brunschweiger A., Brummer A., Guennewig B., Mittal N., et al. miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol. 2014;advance online publication: