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




Illumina Library prep and Array Kit Selector


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


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: