{"entity": "researcher", "timestamp": "2026-08-20T20:28:35.113Z", "family": "Kasukawa", "given": "Takeya", "initials": "T", "orcid": "0000-0001-5085-0802", "affiliations": ["RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3"}}, "publications": [{"entity": "publication", "iuid": "07172111441645cb84cf0dcbc8a39a5a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07172111441645cb84cf0dcbc8a39a5a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07172111441645cb84cf0dcbc8a39a5a"}}, "title": "Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.", "authors": [{"family": "Kang", "given": "Wenjing", "initials": "W", "orcid": "0000-0001-8732-9631", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dd251e7961740f28c25a0580ec314cb.json"}}, {"family": "Yip", "given": "Wing Hin", "initials": "WH", "orcid": "0000-0002-4282-9453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4078204293b34e1c99f0ebd6bee0e732.json"}}, {"family": "Li-Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26e2947dca1e4467aef5342387c5ca7d.json"}}, {"family": "Pedrotti", "given": "Simona", "initials": "S", "orcid": "0000-0001-9502-8556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb6ce1669fc847c5b77fdd25cecd176e.json"}}, {"family": "Yaghi", "given": "Andrea Abou", "initials": "AA"}, {"family": "Murata", "given": "Mitsuyoshi", "initials": "M", "orcid": "0000-0001-9706-8797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604c59620bf844d29dc71c61c40f7bb8.json"}}, {"family": "Salviati", "given": "Lorenzo", "initials": "L", "orcid": "0000-0001-5467-2003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4da8fe43b8474e509e9d83e114e70f91.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Zhang", "given": "Yali", "initials": "Y", "orcid": "0009-0005-8066-1224", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/64d782b175424aca9e73a04890eb64ad.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M"}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F"}, {"family": "Shu", "given": "Xufeng", "initials": "X", "orcid": "0009-0009-0984-5417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f17d670db1f426a9ecaaaaea97a52f5.json"}}, {"family": "Pracana", "given": "Rodrigo", "initials": "R", "orcid": "0000-0003-2492-4067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beea520d340947cb90f1c60bf060feb2.json"}}, {"family": "Shin", "given": "Jay W", "initials": "JW", "orcid": "0000-0003-4037-3533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49d50db4d37d44b4bb8a8f361cbeb2e5.json"}}, {"family": "Kasukawa", "given": "Takeya", "initials": "T", "orcid": "0000-0001-5085-0802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3.json"}}, {"family": "Yip", "given": "Chi Wai", "initials": "CW", "orcid": "0000-0003-3327-5695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a8cd02560534539a2d7cfdd5ef2cf6b.json"}}, {"family": "Kato", "given": "Masaki", "initials": "M", "orcid": "0009-0006-0846-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384c4d198690412589c72779f0794358.json"}}, {"family": "Takahashi", "given": "Hazuki", "initials": "H", "orcid": "0000-0001-7315-7349", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d834f1581a6b451bb1954d7743a566ab.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8da7a1f8524d0e812c83b1f5e20ef6.json"}}], "type": "journal article", "published": "2026-05-27", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Chromatin-associated RNAs have been proposed to be important regulators of such changes; however, the type, abundance, and role of these RNAs during neuronal differentiation remain largely unexplored. Here, we integrate multi-omic data generated in the frame of the Functional ANnoTation Of the Mammalian genome (FANTOM6) to chart 3D genome, RNA-DNA contactome, and transcriptome changes occurring during in vitro differentiation of human induced pluripotent stem cells to neural stem cells and neurons. We reveal a previously unreported phenomenon, in which intronic RNAs engage in long-distance contacts with DNA loci distributed all over the genome. These trans-contacting intronic RNAs (TIRs) are produced from exceptionally long (mean length: 750 kilobases, kb) protein-coding genes that carry ultra-long introns and are selectively expressed in neurons. We show that TIRs do not undergo rapid co-transcriptional degradation but rather accumulate in the nucleus of neuronal cells, forming large 'dot clouds' around their source loci and spreading across the nucleus, as visualized by single-molecule RNA fluorescence in situ hybridization. TIRs engage in contacts with a set of genomic regions (TIR-contacted regions or TIRCs) that carry much shorter (mean length: ~30 kb) neuronally expressed genes forming high-connectivity hubs. We also show that the expression of genes within TIRCs contacted by the same set of TIRs is highly co-varied, and that TIR source genes, especially their introns, are enriched in genetic risk loci for neurodevelopmental and neuropsychiatric disorders. Our findings point to a functional role of the persistence of long intronic RNAs in the nucleus of neuronal cells and might contribute to explain why neurons uniquely express many ultra-long genes. We propose a model in which TIRs form pan-nuclear scaffolds-which we propose to name introsomes-that constitute a dynamically self-renewing regulatory layer, where transcription itself continuously regenerates the very scaffold that organizes genome function in neurons, and that might be involved in the pathogenesis of neurodevelopmental and neuropsychiatric disorders.", "doi": "10.1101/2025.03.13.641826", "pmid": "42244686", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC13232347"}, {"db": "pii", "key": "2025.03.13.641826"}], "notes": [], "created": "2026-08-20T11:01:31.285Z", "modified": "2026-08-20T11:01:31.656Z"}, {"entity": "publication", "iuid": "05a79d3c7acb4d1fa8f1b246ce355de5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05a79d3c7acb4d1fa8f1b246ce355de5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05a79d3c7acb4d1fa8f1b246ce355de5"}}, "title": "Genomic codes governing enhancer RNA fate", "authors": [{"family": "Yip", "given": "Chi Wai", "initials": "CW", "orcid": "0000-0003-3327-5695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a8cd02560534539a2d7cfdd5ef2cf6b.json"}}, {"family": "Parr", "given": "Callum", "initials": "C"}, {"family": "Takahashi", "given": "Hazuki", "initials": "H", "orcid": "0000-0001-7315-7349", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d834f1581a6b451bb1954d7743a566ab.json"}}, {"family": "Yasuzawa", "given": "Kayoko", "initials": "K"}, {"family": "Valentine", "given": "Matthew", "initials": "M"}, {"family": "Nishiyori-Sueki", "given": "Hiromi", "initials": "H"}, {"family": "Ugolini", "given": "Camilla", "initials": "C"}, {"family": "Ranzani", "given": "Valeria", "initials": "V"}, {"family": "Murata", "given": "Mitsuyoshi", "initials": "M"}, {"family": "Kato", "given": "Masaki", "initials": "M", "orcid": "0009-0006-0846-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384c4d198690412589c72779f0794358.json"}}, {"family": "Kang", "given": "Wenjing", "initials": "W", "orcid": "0000-0001-8732-9631", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dd251e7961740f28c25a0580ec314cb.json"}}, {"family": "Fois", "given": "Giulia", "initials": "G", "orcid": "0009-0008-3839-0055", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff9283f31524edcbd15203dddf98429.json"}}, {"family": "Yip", "given": "Wing Hin", "initials": "WH", "orcid": "0000-0002-4282-9453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4078204293b34e1c99f0ebd6bee0e732.json"}}, {"family": "Shibayama", "given": "Youtaro", "initials": "Y"}, {"family": "Sim", "given": "Andre Darah", "initials": "AD"}, {"family": "Chen", "given": "Ying", "initials": "Y"}, {"family": "Shu", "given": "Xufeng", "initials": "X"}, {"family": "Moody", "given": "Jonathan", "initials": "J"}, {"family": "Umarov", "given": "Ramzan", "initials": "R"}, {"family": "Yang", "given": "Manli", "initials": "M"}, {"family": "Lambolez", "given": "Alice", "initials": "A", "orcid": "0000-0003-4227-0888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f7b1becde604e2e966ff14544473f28.json"}}, {"family": "Chang", "given": "Jen Chien", "initials": "JC"}, {"family": "Pandolfini", "given": "Luca", "initials": "L", "orcid": "0000-0003-1444-8167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6a6fe845ea54ff4a82eeac6b64c448c.json"}}, {"family": "Kawashima", "given": "Tsugumi", "initials": "T"}, {"family": "Tagami", "given": "Michihira", "initials": "M"}, {"family": "Nobusada", "given": "Tomoe", "initials": "T"}, {"family": "Kouno", "given": "Tsukasa", "initials": "T"}, {"family": "Alfonso-Gonzalez", "given": "Carlos", "initials": "C"}, {"family": "Pracana", "given": "Rodrigo", "initials": "R", "orcid": "0000-0003-2492-4067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beea520d340947cb90f1c60bf060feb2.json"}}, {"family": "Silva", "given": "Raquel Sofia", "initials": "RS"}, {"family": "Albanese", "given": "Roberto", "initials": "R"}, {"family": "Dossena", "given": "Francesco", "initials": "F"}, {"family": "Haberman", "given": "Nejc", "initials": "N"}, {"family": "Ozaki", "given": "Kokoro", "initials": "K"}, {"family": "Kasukawa", "given": "Takeya", "initials": "T", "orcid": "0000-0001-5085-0802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3.json"}}, {"family": "Lenhard", "given": "Boris", "initials": "B", "orcid": "0000-0002-1114-1509", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/938595001de64507a66e000512ce65cc.json"}}, {"family": "Frith", "given": "Martin", "initials": "M"}, {"family": "Bodega", "given": "Beatrice", "initials": "B"}, {"family": "Nicassio", "given": "Francesco", "initials": "F"}, {"family": "Calviello", "given": "Lorenzo", "initials": "L"}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Legnini", "given": "Ivano", "initials": "I"}, {"family": "Hilgers", "given": "Val\u00e9rie", "initials": "V", "orcid": "0000-0002-4551-0931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d963b81d5134925a791097984e963a7.json"}}, {"family": "Gustincich", "given": "Stefano", "initials": "S", "orcid": "0000-0002-2749-2514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8cd76175c77e4ddca5729c104c3ebd68.json"}}, {"family": "G\u00f6ke", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-0825-4991", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff376f0b4f644996932b7a0a9149206e.json"}}, {"family": "Lecellier", "given": "Charles Henri", "initials": "CH"}, {"family": "Shin", "given": "Jay W", "initials": "JW", "orcid": "0000-0003-4037-3533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49d50db4d37d44b4bb8a8f361cbeb2e5.json"}}, {"family": "Hon", "given": "Chung Chau", "initials": "CC", "orcid": "0000-0002-3741-7577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/deb8e3e3a9624fd2aa709084b58a09e6.json"}}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}], "type": "posted-content", "published": "2024-10-31", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.10.31.620483", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:59:08.159Z", "modified": "2026-08-20T10:59:08.788Z"}, {"entity": "publication", "iuid": "188ae3ff56ce4afba1425736a4b14ee1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/188ae3ff56ce4afba1425736a4b14ee1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/188ae3ff56ce4afba1425736a4b14ee1"}}, "title": "Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.", "authors": [{"family": "Grapotte", "given": "Mathys", "initials": "M"}, {"family": "Saraswat", "given": "Manu", "initials": "M"}, {"family": "Bessi\u00e8re", "given": "Chlo\u00e9", "initials": "C"}, {"family": "Menichelli", "given": "Christophe", "initials": "C", "orcid": "0000-0001-9161-3715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce5001ed87714cc09feedff1c6d793c4.json"}}, {"family": "Ramilowski", "given": "Jordan A", "initials": "JA", "orcid": "0000-0002-3156-6416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1b7cbea9c5c41d88b8ec2b956dc6bcf.json"}}, {"family": "Severin", "given": "Jessica", "initials": "J", "orcid": "0000-0003-1274-208X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc1e076b001f4f70854816102ca00fa4.json"}}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y", "orcid": "0000-0002-0561-2802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77e22fa2db124b93a87b8da206784330.json"}}, {"family": "Itoh", "given": "Masayoshi", "initials": "M", "orcid": "0000-0002-1772-318X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5c390e164054128ab39fb3942bc259d.json"}}, {"family": "Tagami", "given": "Michihira", "initials": "M"}, {"family": "Murata", "given": "Mitsuyoshi", "initials": "M"}, {"family": "Kojima-Ishiyama", "given": "Miki", "initials": "M"}, {"family": "Noma", "given": "Shohei", "initials": "S"}, {"family": "Noguchi", "given": "Shuhei", "initials": "S"}, {"family": "Kasukawa", "given": "Takeya", "initials": "T", "orcid": "0000-0001-5085-0802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3.json"}}, {"family": "Hasegawa", "given": "Akira", "initials": "A"}, {"family": "Suzuki", "given": "Harukazu", "initials": "H", "orcid": "0000-0002-8087-0836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e6cc95987e54a33ade62ef46426620b.json"}}, {"family": "Nishiyori-Sueki", "given": "Hiromi", "initials": "H"}, {"family": "Frith", "given": "Martin C", "initials": "MC"}, {"family": "FANTOM consortium", "given": "", "initials": ""}, {"family": "Chatelain", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}, {"family": "de Hoon", "given": "Michiel J L", "initials": "MJL", "orcid": "0000-0003-0489-2352", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/568a5ee5b57345ad832af833e3589fee.json"}}, {"family": "Wasserman", "given": "Wyeth W", "initials": "WW", "orcid": "0000-0001-6098-6412", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3d6a75d678545a3bd9c6957103fe3d9.json"}}, {"family": "Br\u00e9h\u00e9lin", "given": "Laurent", "initials": "L", "orcid": "0000-0002-2582-2831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63a68addc37948d68933e575affbf45b.json"}}, {"family": "Lecellier", "given": "Charles-Henri", "initials": "CH", "orcid": "0000-0002-0229-5434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85e9d470fd584a45b66ff2faf93f1e33.json"}}], "type": "published erratum", "published": "2022-03-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "1200", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-022-28758-y", "pmid": "35232988", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8888638"}, {"db": "pii", "key": "10.1038/s41467-022-28758-y"}], "notes": [], "created": "2026-08-20T08:51:50.629Z", "modified": "2026-08-20T08:51:50.746Z"}, {"entity": "publication", "iuid": "e60d6c083e424625acf05cedbe0e1eff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e60d6c083e424625acf05cedbe0e1eff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e60d6c083e424625acf05cedbe0e1eff"}}, "title": "Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.", "authors": [{"family": "Grapotte", "given": "Mathys", "initials": "M"}, {"family": "Saraswat", "given": "Manu", "initials": "M"}, {"family": "Bessi\u00e8re", "given": "Chlo\u00e9", "initials": "C"}, {"family": "Menichelli", "given": "Christophe", "initials": "C", "orcid": "0000-0001-9161-3715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce5001ed87714cc09feedff1c6d793c4.json"}}, {"family": "Ramilowski", "given": "Jordan A", "initials": "JA", "orcid": "0000-0002-3156-6416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1b7cbea9c5c41d88b8ec2b956dc6bcf.json"}}, {"family": "Severin", "given": "Jessica", "initials": "J", "orcid": "0000-0003-1274-208X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc1e076b001f4f70854816102ca00fa4.json"}}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y", "orcid": "0000-0002-0561-2802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77e22fa2db124b93a87b8da206784330.json"}}, {"family": "Itoh", "given": "Masayoshi", "initials": "M", "orcid": "0000-0002-1772-318X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5c390e164054128ab39fb3942bc259d.json"}}, {"family": "Tagami", "given": "Michihira", "initials": "M"}, {"family": "Murata", "given": "Mitsuyoshi", "initials": "M"}, {"family": "Kojima-Ishiyama", "given": "Miki", "initials": "M"}, {"family": "Noma", "given": "Shohei", "initials": "S"}, {"family": "Noguchi", "given": "Shuhei", "initials": "S"}, {"family": "Kasukawa", "given": "Takeya", "initials": "T", "orcid": "0000-0001-5085-0802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3.json"}}, {"family": "Hasegawa", "given": "Akira", "initials": "A"}, {"family": "Suzuki", "given": "Harukazu", "initials": "H", "orcid": "0000-0002-8087-0836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e6cc95987e54a33ade62ef46426620b.json"}}, {"family": "Nishiyori-Sueki", "given": "Hiromi", "initials": "H"}, {"family": "Frith", "given": "Martin C", "initials": "MC"}, {"family": "FANTOM consortium", "given": "", "initials": ""}, {"family": "Chatelain", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}, {"family": "de Hoon", "given": "Michiel J L", "initials": "MJL", "orcid": "0000-0003-0489-2352", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/568a5ee5b57345ad832af833e3589fee.json"}}, {"family": "Wasserman", "given": "Wyeth W", "initials": "WW", "orcid": "0000-0001-6098-6412", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3d6a75d678545a3bd9c6957103fe3d9.json"}}, {"family": "Br\u00e9h\u00e9lin", "given": "Laurent", "initials": "L", "orcid": "0000-0002-2582-2831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63a68addc37948d68933e575affbf45b.json"}}, {"family": "Lecellier", "given": "Charles-Henri", "initials": "CH", "orcid": "0000-0002-0229-5434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85e9d470fd584a45b66ff2faf93f1e33.json"}}], "type": "journal article", "published": "2021-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3297", "issn-l": "2041-1723"}, "abstract": "Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.", "doi": "10.1038/s41467-021-23143-7", "pmid": "34078885", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8172540"}, {"db": "pii", "key": "10.1038/s41467-021-23143-7"}], "notes": [], "created": "2026-08-20T08:51:30.723Z", "modified": "2026-08-20T08:51:31.181Z"}]}