{"entity": "researcher", "timestamp": "2026-08-20T19:55:43.966Z", "family": "Murata", "given": "Mitsuyoshi", "initials": "M", "orcid": "0000-0001-9706-8797", "affiliations": ["RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/604c59620bf844d29dc71c61c40f7bb8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/604c59620bf844d29dc71c61c40f7bb8"}}, "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"}]}