{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Fang X"],"funding":["Fundamental Research Funds for the Central Universities","National Natural Science Foundation of China","National Science and Technology Major Project"],"pubmed_abstract":["Pseudouridine (Ψ) is one of the most abundant RNA modifications, playing crucial roles in various biological processes. Identifying Ψ sites is vital for understanding their functions. In this study, we proposed a novel method for identifying Ψ sites with an improved signal-to-noise ratio. This method, called RNA exonuclease-assisted identification of pseudouridine sites (RIPS), combines specific CMC-labeling of Ψ sites with an exonuclease-assisted digestion strategy for the detection of Ψ sites. Utilizing exonuclease XRN1 to digest RNA strands not labeled by CMC, RIPS significantly reduces the background signal from unlabeled strands and enhances the positive signal of Ψ sites labeled by CMC, which terminates exonuclease digestion. As a result, we can enrich Ψ sites and identify them at si"],"journal":["Chemical science"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11515940"],"repository":["biostudies-literature"],"pubmed_title":["Exonuclease-assisted enrichment and base resolution analysis of pseudouridine in single-stranded RNA."],"pmcid":["PMC11515940"],"funding_grant_id":["22377096","21721005","2042023kfyq05","2042023kf0118","92253202","92153303","22177087","2023YFC3402200"],"pubmed_authors":["Fang X","Yang W","Sun M","Zhao R","Lu Z","Weng X","Mo J","Wang Y","Zhou X"],"additional_accession":[]},"is_claimable":false,"name":"Exonuclease-assisted enrichment and base resolution analysis of pseudouridine in single-stranded RNA.","description":"Pseudouridine (Ψ) is one of the most abundant RNA modifications, playing crucial roles in various biological processes. Identifying Ψ sites is vital for understanding their functions. In this study, we proposed a novel method for identifying Ψ sites with an improved signal-to-noise ratio. This method, called RNA exonuclease-assisted identification of pseudouridine sites (RIPS), combines specific CMC-labeling of Ψ sites with an exonuclease-assisted digestion strategy for the detection of Ψ sites. Utilizing exonuclease XRN1 to digest RNA strands not labeled by CMC, RIPS significantly reduces the background signal from unlabeled strands and enhances the positive signal of Ψ sites labeled by CMC, which terminates exonuclease digestion. As a result, we can enrich Ψ sites and identify them at si","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Oct","modification":"2026-07-15T14:51:56.684Z","creation":"2025-04-06T14:23:18.105Z"},"accession":"S-EPMC11515940","cross_references":{"pubmed":["39479159"],"doi":["10.1039/d4sc03576c"]}}