{"doi":"10.1101/2024.01.31.578250","title":"Integrative analysis of nanopore direct RNA sequencing data reveals a role of PUS7-dependent pseudouridylation in regulation of m <sup>6</sup> A and m <sup>5</sup> C modifications","abstract":"Abstract Understanding the interactions between different RNA modifications is essential for unraveling their biological functions. Here, we report NanoPsiPy, a computational pipeline that employs nanopore direct RNA sequencing to identify pseudouridine (Ψ) sites and quantify their levels at single-nucleotide resolution. We validated NanoPsiPy by transcriptome-wide profiling of PUS7-dependent Ψ sites in poly-A RNA and rRNA. NanoPsiPy leverages Ψ-induced U-to-C basecalling errors in nanopore sequencing data, allowing detection of both low and high stoichiometric Ψ sites. We identified 8,624 PUS7-dependent Ψ sites in 1,246 mRNAs encoding proteins associated with ribosome biogenesis, translation, and energy metabolism. Importantly, integrative analysis revealed that PUS7 knockdown increases global mRNA N 6 -methyladenosine (m 6 A) and 5-methylcytosine (m 5 C) levels, suggesting an antagonistic relationship between Ψ and these modifications. Our study underscores the potential of nanopore direct RNA sequencing in revealing the co-regulation of RNA modifications and the capacity of NanoPsiPy in analyzing pseudouridylation and its impact on other RNA modifications.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484799,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9409,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1326950,"name":"Anirban Kundu","orcid":"0000-0002-0087-4117","position":1,"is_corresponding":false},{"id":866846,"name":"Anamika Gupta","orcid":null,"position":2,"is_corresponding":false},{"id":1070689,"name":"Jane Ding","orcid":"0009-0006-3539-8145","position":3,"is_corresponding":false},{"id":237222,"name":"Andrew Gibson","orcid":"0000-0001-9653-3298","position":4,"is_corresponding":false},{"id":1327415,"name":"Sanjay Varma RudraRaju","orcid":null,"position":5,"is_corresponding":false},{"id":356407,"name":"Sunil Sudarshan","orcid":"0000-0001-7257-6277","position":6,"is_corresponding":false},{"id":1327416,"name":"Han-Fei Ding","orcid":null,"position":7,"is_corresponding":false},{"id":63579,"name":"Mohit Bansal","orcid":"0000-0001-5522-1351","position":0,"is_corresponding":true}],"reference_count":31,"raw_metadata":null,"created_at":"2026-07-19T02:07:42.971417Z","pmid":"38352483","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}