GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins

• Published in: Genome Biology Vol. 24; no. 1; pp. 281 - 30
• Main Authors: Zhu, Wandi S, Litterman, Adam J, Sekhon, Harshaan S, Kageyama, Robin, Arce, Maya M, Taylor, Kimberly E, Zhao, Wenxue, Criswell, Lindsey A, Zaitlen, Noah, Erle, David J, Ansel, K Mark
• Format: Journal Article
• Language: English
• Published: England BioMed Central 07-12-2023; BMC
• Subjects: Animals; Binding sites; Binding Sites - genetics; CD5 antigen; Cis-regulatory elements; Gene expression; Humans; Immunoprecipitation; Lymphocytes; Lymphocytes T; Methods; Mice; Phylogenetics; Post-transcriptional regulation; Protein Binding; Protein purification; Proteins; Regulatory sequences; RNA - metabolism; RNA-binding protein; RNA-binding proteins (RBP); RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Stat6 protein; T cells; Transcriptome; Transcriptomes; Post-transcriptional regulation; RNA-binding proteins (RBP); T cells; Cis-regulatory elements
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-023-03125-2

GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.