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Article Dans Une Revue Nucleic Acids Research Année : 2018

Monitored eCLIP: high accuracy mapping of RNA-protein interactions

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Résumé

CLIP-seq methods provide transcriptome-wide snapshots of RNA-protein interactions in live cells. Reverse transcriptases stopping at cross-linked nucleotides sign for RNA-protein binding sites. Reading through cross-linked positions results in false binding site assignments. In the 'monitored enhanced CLIP' (meCLIP) method, a barcoded biotiny-lated linker is ligated at the 5 end of cross-linked RNA fragments to purify RNA prior to the reverse transcription. cDNAs keeping the barcode sequence correspond to reverse transcription read-throughs. Read through occurs in unpredictable proportions, representing up to one fourth of total reads. Filtering out those reads strongly improves reliability and precision in protein binding site assignment.
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Dates et versions

hal-02387433 , version 1 (29-11-2019)

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Rémi Hocq, Janio Paternina, Quentin Alasseur, Auguste Genovesio, Hervé Le Hir. Monitored eCLIP: high accuracy mapping of RNA-protein interactions. Nucleic Acids Research, 2018, 46 (21), pp.11553-11565. ⟨10.1093/nar/gky858⟩. ⟨hal-02387433⟩

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