@inbook{b8488f8e2d9e45e6a3e3daa7614c47e3,
title = "Identification of mirna-target rna interactions using clash",
abstract = "We present a detailed protocol for the experimental identifi cation of miRNA-target RNA interaction sites using c ross-linking, l igation, a nd s equencing of h ybrids (CLASH). The basis of the technique is the purifi cation of UV-stabilized Argonaute (AGO)–RNA complexes assembled in living cells, with subsequent ligation of AGO-associated RNA-RNA duplexes to form chimeric RNAs. Following cDNA synthesis, DNA library preparation and high-throughput sequencing, interacting RNA molecules are unambiguously identifi ed as chimeric reads in bioinformatic analysis of sequencing data. CLASH potentially recovers any RNA duplex that is bound by RNA-binding protein, so modifi ed approaches would be suitable for the identifi cation of many other inter- and intramolecular RNA-RNA interactions. Since CLASH analysis is independent of bioinformatic predictions it allows the identifi cation and analysis of RNA targeting rules in an unbiased way.",
keywords = "argonaute, CLASH, CLIP, MicroRNA, MiRNA target identifi cation, Protein-RNA interaction s, RNA cross-linking, RNA-RNA interactions, UV cross-linking",
author = "Aleksandra Helwak and David Tollervey",
year = "2016",
month = jan,
day = "1",
doi = "10.1007/978-1-4939-3067-8_14",
language = "English",
volume = "1358",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "229--251",
booktitle = "Methods in Molecular Biology",
}