sCLIP—an integrated platform to study RNA–protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs

2017/02/23 by Yulia Kargapolova, Michal Levin, Karl J. Lackner +1 · 2 citations
Biochemistry, Genetics and Molecular Biology · #RNA Research and Splicing #RNA modifications and cancer #RNA and protein synthesis mechanisms #Biology #RNA #RNA-binding protein #Immunoprecipitation #Computational biology #Small nuclear RNA #Small nucleolar RNA #Genetics #RNA splicing #Non-coding RNA #Regulation of gene expression #Gene

paper · pdf · doi:10.1093/nar/gkx152

openalex publication_date 2017/02/23 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally, it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RBP-protein interaction landscapes in health and disease.

Citations

• Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
• Prp43 Bound at Different Sites on the Pre-rRNA Performs Distinct Functions in Ribosome Synthesis
• Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
• Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end
• RNA-binding proteins in human genetic disease

Cited by

• Advances in CLIP Technologies for Studies of Protein-RNA Interactions
• Cross-linking immunoprecipitation [wikipedia]

Related

• A large-scale binding and functional map of human RNA-binding proteins
• CLIP (Cross-Linking and Immunoprecipitation) Identification of RNAs Bound by a Specific Protein
• Analysis of Protein–RNA Interactions with Single‐Nucleotide Resolution Using iCLIP and Next‐Generation Sequencing
• Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks
• PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins