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
- CLASH-Seq: Kudla G., Granneman S., Hahn D., Beggs J. D. and Tollervey D. (2011) Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc Natl Acad Sci U S A 108: 10010-10015
- 1. Imig J., Brunschweiger A., Brummer A., et al. miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol. 2015;11:107-114
- 2. Hausser J. and Zavolan M. Identification and consequences of miRNA-target interactions--beyond repression of gene expression. Nat Rev Genet. 2014;15:599-612
- 3. Lu Z., Zhang Q. C., Lee B., et al. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016;165:1267-1279
- 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