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

Autor: Zhu WS; Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA., Litterman AJ; Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA., Sekhon HS; Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.; University of California Berkeley, Berkeley, CA, USA., Kageyama R; Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA., Arce MM; Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA., Taylor KE; Department of Medicine, University of California San Francisco, San Francisco, USA.; Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA., Zhao W; Department of Medicine, University of California San Francisco, San Francisco, USA.; Lung Biology Center, University of California San Francisco, San Francisco, USA.; School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China., Criswell LA; Department of Medicine, University of California San Francisco, San Francisco, USA.; Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA., Zaitlen N; Department of Medicine, University of California San Francisco, San Francisco, USA.; Lung Biology Center, University of California San Francisco, San Francisco, USA., Erle DJ; Department of Medicine, University of California San Francisco, San Francisco, USA.; Lung Biology Center, University of California San Francisco, San Francisco, USA., Ansel KM; Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA. Mark.Ansel@ucsf.edu.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2023 Dec 07; Vol. 24 (1), pp. 281. Date of Electronic Publication: 2023 Dec 07.
DOI: 10.1186/s13059-023-03125-2
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
Externí odkaz: