{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T16:34:49Z","timestamp":1789576489169,"version":"build-2803163510"},"reference-count":17,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>\n                    Understanding the host transcriptional and epitranscriptomic response to\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (Mtb) infection is vital for decoding mechanisms of immune evasion and persistence. Here, we employed Oxford Nanopore Technologies (ONT)-based direct RNA sequencing (DRS) on human THP-1 macrophages infected with Mtb. This third-generation sequencing approach enables full-length transcript analysis and simultaneous detection of RNA modifications without reverse transcription or amplification. We uncovered extensive alternative splicing events, widespread shortening of poly(A) tails, and significant shifts in usage of proximal versus distal polyadenylation sites upon infection. Furthermore, we identified infection-induced changes in m6A, m5C, pseudouridine (\u03a8), and inosine modifications across different genomic regions, with distinct motif preference and distribution shifts. Pathway enrichment analyses revealed these changes were associated with host responses to infection, inflammation, metabolism, and apoptosis. Our study provides a comprehensive epitranscriptomic landscape of macrophage responses to Mtb infection and highlights potential regulatory layers governing host-pathogen interaction.\n                  <\/jats:p>","DOI":"10.3389\/fcimb.2025.1689553","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T06:32:02Z","timestamp":1762842722000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Direct RNA sequencing reveals multilayered epitranscriptomic remodeling in macrophages upon Mtb infection"],"prefix":"10.3389","volume":"15","author":[{"given":"Ren-Chao","family":"Zou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiuhong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianming","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiawei","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gendis.2021.12.005","article-title":"Systematic analysis of clinical relevance and molecular characterization of m(6)A in COVID-19 patients","volume":"9","author":"An","year":"2022","journal-title":"Genes Dis"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.29466","article-title":"Dynamic m(6) A profiles reveal the role of YTHDC2-TLR2 signaling axis in Talaromyces marneffei infection","volume":"96","author":"Chu","year":"2024","journal-title":"J. Med. Virol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/j.gpb.2021.11.001","article-title":"Specific regulation of m(6)A by SRSF7 promotes the progression of glioblastoma","volume":"21","author":"Cun","year":"2023","journal-title":"Genomics Proteomics Bioinf."},{"key":"B4","doi-asserted-by":"publisher","first-page":"107325","DOI":"10.1016\/j.ijid.2024.107325","article-title":"Insights from the 2024 WHO Global Tuberculosis Report - More Comprehensive Action, Innovation, and Investments required for achieving WHO End TB goals","volume":"150","author":"Goletti","year":"2025","journal-title":"Int. J. Infect. Dis."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1038\/s41592-022-01666-1","article-title":"Detection of m6A from direct RNA sequencing using a multiple instance learning framework","volume":"19","author":"Hendra","year":"2022","journal-title":"Nat. Methods"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.73984.sa2","article-title":"Mycobacterium tuberculosis canonical virulence factors interfere with a late component of the TLR2 response","volume":"10","author":"Hinman","year":"2021","journal-title":"Elife"},{"key":"B7","doi-asserted-by":"publisher","first-page":"3971","DOI":"10.1093\/nar\/gkad177","article-title":"A dual-purpose polymerase engineered for direct sequencing of pseudouridine and queuosine","volume":"51","author":"Huber","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B8","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1007\/s11262-020-01746-4","article-title":"Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions","volume":"56","author":"Li","year":"2020","journal-title":"Virus Genes"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1093\/gpbjnl\/qzae039","article-title":"Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level","volume":"22","author":"Li","year":"2024","journal-title":"Genomics Proteomics Bioinf."},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1093\/gpbjnl\/qzae052","article-title":"Pan-cancer analysis reveals m6A variation and cell-specific regulatory network in different cancer types","volume":"22","author":"Lin","year":"2024","journal-title":"Genomics Proteomics Bioinf"},{"key":"B11","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1007\/978-1-0716-1374-0_3","article-title":"EpiNano: detection of m(6)A RNA modifications using oxford nanopore direct RNA sequencing","volume":"2298","author":"Liu","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/s41592-022-01513-3","article-title":"Direct identification of A-to-I editing sites with nanopore native RNA sequencing","volume":"19","author":"Nguyen","year":"2022","journal-title":"Nat. Methods"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.49658","article-title":"Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification","volume":"9","author":"Parker","year":"2020","journal-title":"Elife"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.756288","article-title":"Genome-wide profiling reveals alternative polyadenylation of innate immune-related mRNA in patients with COVID-19","volume":"12","author":"Sanqi","year":"2021","journal-title":"Front. Immunol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1038\/s41467-023-35858-w","article-title":"Semi-quantitative detection of pseudouridine modifications and type I\/II hypermodifications in human mRNAs using direct long-read sequencing","volume":"14","author":"Tavakoli","year":"2023","journal-title":"Nat. Commun."},{"key":"B16","article-title":"Global Tuberculosis Report 2023","year":"2023"},{"key":"B17","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.ymeth.2022.04.003","article-title":"Primary sequence-assisted prediction of m(6)A RNA methylation sites from Oxford nanopore direct RNA sequencing data","volume":"203","author":"Zhang","year":"2022","journal-title":"Methods"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1689553\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T06:32:02Z","timestamp":1762842722000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1689553\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,11]]},"references-count":17,"alternative-id":["10.3389\/fcimb.2025.1689553"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1689553","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,11]]},"article-number":"1689553"}}