{"doi":"10.1093/narmme/ugae016","title":"Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling","abstract":"Abstract A majority of human genes produce non-protein-coding RNA (ncRNA), and some have roles in development and disease. Neither ncRNA nor human skeletal muscle is ideally studied using short-read sequencing, so we used a customized RNA pipeline and network modelling to study cell-type specific ncRNA responses during muscle growth at scale. We completed five human resistance-training studies (n = 144 subjects), identifying 61% who successfully accrued muscle-mass. We produced 288 transcriptome-wide profiles and found 110 ncRNAs linked to muscle growth in vivo, while a transcriptome-driven network model demonstrated interactions via a number of discrete functional pathways and single-cell types. This analysis included established hypertrophy-related ncRNAs, including CYTOR—which was leukocyte-associated (false discovery rate [FDR] = 4.9 × 10−7). Novel hypertrophy-linked ncRNAs included PPP1CB-DT (myofibril assembly genes, FDR = 8.15 × 10−8), and EEF1A1P24 and TMSB4XP8 (vascular remodelling and angiogenesis genes, FDR = 2.77 × 10−5). We also discovered that hypertrophy lncRNA MYREM shows a specific myonuclear expression pattern in vivo. Our multi-layered analyses established that single-cell-associated ncRNA are identifiable from bulk muscle transcriptomic data and that hypertrophy-linked ncRNA genes mediate their association with muscle growth via multiple cell types and a set of interacting pathways.","journal":"NAR Molecular Medicine","year":2024,"id":439239,"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":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.7179,"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":1126931,"name":"Changhyun Lim","orcid":"0000-0002-5437-8063","position":1,"is_corresponding":false},{"id":1249879,"name":"Tanner Stokes","orcid":"0009-0002-2614-6713","position":2,"is_corresponding":false},{"id":1250501,"name":"Jalil-Ahmad Sharif","orcid":null,"position":3,"is_corresponding":false},{"id":1250502,"name":"Vagif Zeynalli","orcid":null,"position":4,"is_corresponding":false},{"id":1249880,"name":"Lucas Wiens","orcid":"0000-0002-4423-4461","position":5,"is_corresponding":false},{"id":1213998,"name":"Alysha C. D’Souza","orcid":null,"position":6,"is_corresponding":false},{"id":1250503,"name":"Lauren M. Colenso‐Semple","orcid":null,"position":7,"is_corresponding":false},{"id":878734,"name":"James McKendry","orcid":"0000-0002-9951-0590","position":8,"is_corresponding":false},{"id":1015999,"name":"Robert W. Morton","orcid":"0000-0003-0099-4167","position":9,"is_corresponding":false},{"id":1249881,"name":"Cameron J. Mitchell","orcid":"0000-0003-3843-6806","position":10,"is_corresponding":false},{"id":1249882,"name":"Sara Y. Oikawa","orcid":"0000-0002-4280-4619","position":11,"is_corresponding":false},{"id":279165,"name":"Claes Wahlestedt","orcid":"0000-0003-4471-5916","position":12,"is_corresponding":false},{"id":906792,"name":"J. Paul Chapple","orcid":"0000-0003-1876-1505","position":13,"is_corresponding":false},{"id":1249883,"name":"Chris McGlory","orcid":"0000-0003-4853-4960","position":14,"is_corresponding":false},{"id":674878,"name":"James A. Timmons","orcid":"0000-0002-2255-1220","position":15,"is_corresponding":false},{"id":255964,"name":"Stuart M. Phillips","orcid":"0000-0002-1956-4098","position":16,"is_corresponding":false},{"id":878735,"name":"Jonathan C. Mcleod","orcid":"0000-0002-2471-7482","position":0,"is_corresponding":true}],"reference_count":131,"raw_metadata":null,"created_at":"2026-07-19T02:00:47.992543Z","pmid":"39669123","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":[]}