PRJNA838401
CLLASH reveals the in vivo RNA-RNA interactions recognized by hnRNPK
RNA-RNA interactions associated with various RNA-binding proteins (RBPs) regulate gene expression and critical biological processes. However, identifying RNA interactions associate with specific proteins of interest on a transcriptomic scale still remains challenging. Here we present CLLASH, a biochemical technique for transcriptome-wide identification of intra- and intermolecular RNA-RNA interactions mediated by RBPs. Applying this method in human cells reveals a remarkable landscape of intermolecular RNA interactions recognized by hnRNPK, involving all major classes of ncRNA and mRNA. We validated one new lncRNA-mRNA interaction using single-molecule RNA FISH and miRNA target genes by inhibiting this miRNA and detecting the transcription level of target genes. Our study introduces CLLASH as a widely applicable method for discovering new RNA interactions bound by defined proteins of interest.