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    The HITS-CLIP technique

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    High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation

    High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP, also known as CLIP-Seq) was developed as a genome-wide mean to map protein-RNA binding sites. HITS-CLIP capitalizes on in vivo UV crosslinking of cells or tissues to form covalent bond between RNAs and proteins that are in direct contact. This step is followed by an immunopurification of the RNA-protein complexes of interest and finally next-generation sequencing of the isolated RNA tags.

    HITS-CLIP as been succesfully used  in a wide variety of tissus and organisms and for a wide panel of factors (NOVA1 and NOVA2, PTB, RbFox2, hNRNP C, Ago2…). It has recently been applied in the laboratory of Host-Virus Interactions to identify Argonaute binding sites on HIV-1 RNA (Eckenfelder et al, Nucleic Acid Res. 2017).

    Several variants of the HITS-CLIP protocols have been developed to increase the resolution and efficiency of the technique (PAR-CLIP and iCLIP). Derivatives of this technique have also been developped to identify miRNA bound to their target mRNA (CLASH) or to precisely map N6-Methyladenosine (M6A) locations in mRNA (M6A-CLIP).

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