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DUX4 is a transcription factor, which is normally expressed in the cleavage-stage embryo and regulates gene expression involved in early embryonic development. Recent studies revealed that DUX4 also activates the transcription of repetitive elements such as endogenous retroviruses (ERVs), mammalian apparent long terminal repeat (LTR)-retrotransposons and pericentromeric satellite repeats (Human Satellite II). DUX4-bound ERV sequences also create alternative promoters for genes or long non-coding RNAs, producing fusion transcripts. To further understand transcriptional regulation by DUX4, we performed nanopore long-read direct RNA sequencing (dRNA-seq) of human muscle cells induced by DUX4, because long reads show whole isoforms with greater confidence. We successfully detected differential expression of known DUX4-induced genes and discovered 61 differentially expressed repeat loci, which are near DUX4\u2013ChIP peaks. We also identified 247 gene\u2013ERV fusion transcripts, of which 216 were not reported previously. In addition, long-read dRNA-seq clearly shows that RNA splicing is a common event in DUX4-activated ERV transcripts. Long-read analysis showed non-LTR transposons including Alu elements are also transcribed from LTRs. Our findings revealed further complexity of DUX4-induced ERV transcripts. This catalogue of DUX4-activated repetitive elements may provide useful information to elucidate the pathology of FSHD. Also, our results indicate that nanopore dRNA-seq has complementary strengths to conventional short-read complementary DNA sequencing.<\/jats:p>","DOI":"10.1093\/hmg\/ddab063","type":"journal-article","created":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T15:10:37Z","timestamp":1614179437000},"page":"552-563","source":"Crossref","is-referenced-by-count":25,"title":["Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells"],"prefix":"10.1093","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5036-6858","authenticated-orcid":false,"given":"Satomi","family":"Mitsuhashi","sequence":"first","affiliation":[{"name":"Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Tokyo 113-8510, Japan"},{"name":"Department of Human Genetics, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"So","family":"Nakagawa","sequence":"additional","affiliation":[{"name":"Micro\/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan"},{"name":"Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitsuru","family":"Sasaki-Honda","sequence":"additional","affiliation":[{"name":"Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hidetoshi","family":"Sakurai","sequence":"additional","affiliation":[{"name":"Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin C","family":"Frith","sequence":"additional","affiliation":[{"name":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan"},{"name":"Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan"},{"name":"Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Mitsuhashi","sequence":"additional","affiliation":[{"name":"Micro\/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan"},{"name":"Department of Applied Biochemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,3,9]]},"reference":[{"key":"2021051411364754500_ref1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S0378-1119(99)00267-X","article-title":"Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element","volume":"236","author":"Gabriels","year":"1999","journal-title":"Gene"},{"key":"2021051411364754500_ref2","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1126\/science.1189044","article-title":"A unifying genetic model for facioscapulohumeral muscular dystrophy","volume":"329","author":"Lemmers","year":"2010","journal-title":"Science"},{"key":"2021051411364754500_ref3","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/ng1262","article-title":"Hypomethylation of D4Z4 in 4q-linked and non-4q-linked facioscapulohumeral muscular dystrophy","volume":"35","author":"Overveld","year":"2003","journal-title":"Nat. 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