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TDP-43 regulates RNA splicing, and its dysfunction in neurons is a hallmark of some neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). While an association between TDP-43-dependent cryptic exons and disease pathogenesis has been suggested, an approach to investigate how cryptic exons disrupt transcript isoforms has yet to be established. In this study, we developed IsoRefiner, a novel method for identifying full-length transcript structures using long-read RNA-seq. Leveraging this method, we performed long-read RNA-seq, guided by prior short-read RNA-seq, to comprehensively determine the full-length structures of aberrant transcripts due to TDP-43 dysregulation in human iPSC-derived motor neurons. We identified a novel TDP-43-dependent cryptic exon in the <jats:italic>MNAT1<\/jats:italic> gene, along with its full-length transcript structure. Furthermore, we confirmed the presence of the <jats:italic>MNAT1<\/jats:italic> cryptic exon in patients with ALS and FTD. Our findings deepen understanding of TDP-43 proteinopathy and advance splicing research.<\/jats:p>","DOI":"10.1038\/s42003-025-08463-4","type":"journal-article","created":{"date-parts":[[2025,7,16]],"date-time":"2025-07-16T12:37:17Z","timestamp":1752669437000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Long-read RNA sequencing unveils a novel cryptic exon in MNAT1 along with its full-length transcript structure in TDP-43 proteinopathy"],"prefix":"10.1038","volume":"8","author":[{"given":"Yoshihisa","family":"Tanaka","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naohiro","family":"Sunamura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5013-0052","authenticated-orcid":false,"given":"Rei","family":"Kajitani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7411-2193","authenticated-orcid":false,"given":"Marie","family":"Ikeguchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4895-9686","authenticated-orcid":false,"given":"Ryo","family":"Kunimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,7,16]]},"reference":[{"key":"8463_CR1","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.tig.2018.10.002","volume":"35","author":"M Montes","year":"2019","unstructured":"Montes, M., Sanford, B. 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