Monitored eCLIP: high accuracy mapping of RNA-protein interactions

Rémi Hocq (1) , Janio Paternina (1) , Quentin Alasseur (1) , Auguste Genovesio (1) , Hervé Le Hir (1)

1 IBENS - Institut de biologie de l'ENS Paris

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.

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Biochimie, Biologie Moléculaire

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⟩