CLIP-Seq

cCLIP-Seq: Retrieval of Chimeric Reads from HITS-CLIP (CLIP-Seq) Libraries

Summary This methods chapter describes cCLIP-seq, a computational approach for identifying and retrieving chimeric reads from HITS-CLIP libraries, where a small RNA and its target RNA are co-ligated and sequenced as a single molecule. By resolving these chimeric tags, cCLIP-seq enables direct identification of small RNA binding sites and precise base-pairing profiles at single-nucleotide resolution.

CLIPSeqTools — a novel bioinformatics CLIP-seq analysis suite

Summary CLIPSeqTools is a modular bioinformatics pipeline for the analysis of CLIP-seq data, providing tools for read processing, peak calling, motif analysis, and visualization. The suite enables comprehensive characterization of RNA-binding protein interaction sites across the transcriptome.

FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns

Summary CLIP-seq analysis reveals that FUS, an ALS-associated RNA-binding protein, preferentially binds to highly conserved intronic sequences of genes encoding other RNA-binding proteins in neurons. This autoregulatory network suggests a mechanism by which FUS dysfunction could broadly disrupt neuronal RNA metabolism.

Identification of in vivo, conserved, TAF15 RNA binding sites reveals the impact of TAF15 on the neuronal transcriptome

Summary Using CLIP-seq, this study identifies the in vivo binding sites of TAF15, an ALS-associated RNA-binding protein, across the neuronal transcriptome. The findings reveal evolutionarily conserved binding sites and provide insight into the role of TAF15 in neuronal RNA metabolism.