{"entity": "researcher", "timestamp": "2026-08-20T20:29:16.795Z", "family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "affiliations": ["Department of Women's and Children's Health, Karolinska Institutet, 171 76 Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4"}}, "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": "9787117993cc48c69f47c081feaea41e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9787117993cc48c69f47c081feaea41e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9787117993cc48c69f47c081feaea41e"}}, "title": "Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis", "authors": [{"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/082d532a452346ce94d507b9d8186ccb.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8cc6d65911b84adab955eed1cb47dbe0.json"}}, {"family": "Soldini", "given": "Cristina", "initials": "C"}, {"family": "Alatar", "given": "Shemim", "initials": "S"}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad35ae5b8ff64a6c965030e149a9749d.json"}}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7885bdf463cf41538ea08a35898c1cae.json"}}, {"family": "Molinari", "given": "Maya", "initials": "M"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc126b42b76c456b828eb2d86c7619e4.json"}}, {"family": "Poulet", "given": "Axel", "initials": "A", "orcid": "0000-0002-3415-8960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cdbdf8ec40043bca6f6157fbde8056d.json"}}, {"family": "Watts", "given": "Michelle", "initials": "M", "orcid": "0000-0002-3178-3429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f63c70eaec548e5aaa86e033f5d2207.json"}}, {"family": "Rabkina", "given": "Ielyzaveta", "initials": "I", "orcid": "0000-0001-5890-4115", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f70154226777443e80607201a988d234.json"}}, {"family": "Becker", "given": "Martin", "initials": "M", "orcid": "0000-0001-8442-4246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/517c767452664ae4ba352a9702aebbfa.json"}}, {"family": "Li", "given": "Danyang", "initials": "D", "orcid": "0000-0001-7470-6645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b954078f0053418fb07b876f41700177.json"}}, {"family": "Anderlid", "given": "Britt Marie", "initials": "BM", "orcid": "0000-0002-2488-6024", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181592a5b6445a8873b412cb9830a32.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J", "orcid": "0000-0003-1033-2618", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/782d9f1c46694ba9b911d1ea6d7019f6.json"}}, {"family": "Remnelius", "given": "Karl Lundin", "initials": "KL"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Jacob", "given": "Yannick", "initials": "Y", "orcid": "0000-0003-4741-0755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b96e31cab421475b991a632f9491c51c.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8825c33511418a83eceffdb530dadb.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b1cef698ae749749b4017dbacb9e3db.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8da7a1f8524d0e812c83b1f5e20ef6.json"}}, {"family": "Santini", "given": "Emanuela", "initials": "E", "orcid": "0000-0002-8948-9652", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0871f60791434c2eb639cda18c586879.json"}}, {"family": "Borgkvist", "given": "Anders", "initials": "A", "orcid": "0000-0003-1698-0288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d90df9c8aa584473b6e655c5463bbc88.json"}}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S", "orcid": "0000-0002-4579-4970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a274bd6d9c0f49789bedc115dd1356a3.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4.json"}}], "type": "posted-content", "published": "2022-09-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.09.14.507275", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:14:08.367Z", "modified": "2026-08-20T10:14:08.767Z"}, {"entity": "publication", "iuid": "f9884510a26a46399dbac644e459eefd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f9884510a26a46399dbac644e459eefd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f9884510a26a46399dbac644e459eefd"}}, "title": "Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics", "authors": [{"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad35ae5b8ff64a6c965030e149a9749d.json"}}, {"family": "Becker", "given": "Martin", "initials": "M", "orcid": "0000-0001-8442-4246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/517c767452664ae4ba352a9702aebbfa.json"}}, {"family": "Marques", "given": "C\u00e1tia", "initials": "C"}, {"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8cc6d65911b84adab955eed1cb47dbe0.json"}}, {"family": "Li", "given": "Danyang", "initials": "D", "orcid": "0000-0001-7470-6645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b954078f0053418fb07b876f41700177.json"}}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/082d532a452346ce94d507b9d8186ccb.json"}}, {"family": "Watts", "given": "Michelle Evelyn", "initials": "ME", "orcid": "0000-0002-3178-3429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f63c70eaec548e5aaa86e033f5d2207.json"}}, {"family": "Arora", "given": "Manish", "initials": "M", "orcid": "0000-0002-3350-4657", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/effd70cf5cd54ee09a99e21b00470617.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8825c33511418a83eceffdb530dadb.json"}}, {"family": "Daub", "given": "Carsten Oliver", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}, {"family": "Lanekoff", "given": "Ingela", "initials": "I", "orcid": "0000-0001-9040-3230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122c0ddd06d841fa9c86e3ee1b415cd2.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4.json"}}], "type": "posted-content", "published": "2022-06-28", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.06.27.497311", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:12:20.063Z", "modified": "2026-08-20T10:12:20.386Z"}, {"entity": "publication", "iuid": "8fe4a1d767fc4ad7bc41eb58710cc1bd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8fe4a1d767fc4ad7bc41eb58710cc1bd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8fe4a1d767fc4ad7bc41eb58710cc1bd"}}, "title": "Modeling SHH-driven medulloblastoma with patient iPS cell-derived neural stem cells.", "authors": [{"family": "Susanto", "given": "Evelyn", "initials": "E"}, {"family": "Marin Navarro", "given": "Ana", "initials": "A"}, {"family": "Zhou", "given": "Leilei", "initials": "L"}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0003-3942-6271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63e6602d2807417684239b93eb065a26.json"}}, {"family": "van Bree", "given": "Niek", "initials": "N", "orcid": "0000-0001-5010-3524", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afdb3d47b0be46cbbf7e10f7367f6d7b.json"}}, {"family": "Stantic", "given": "Marina", "initials": "M"}, {"family": "Moslem", "given": "Mohsen", "initials": "M", "orcid": "0000-0002-2440-9586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac548b831c044a53ac324691083df9e1.json"}}, {"family": "Tailor", "given": "Jignesh", "initials": "J"}, {"family": "Rietdijk", "given": "Jonne", "initials": "J"}, {"family": "Zubillaga", "given": "Veronica", "initials": "V", "orcid": "0000-0002-8806-939X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0feb462e3293492bae0e051990b387df.json"}}, {"family": "H\u00fcbner", "given": "Jens-Martin", "initials": "JM"}, {"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "Wolfsberger", "given": "Johanna", "initials": "J"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I", "orcid": "0000-0002-6249-569X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d5a2e976bc84739a957f2b12517df7e.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Magnaldo", "given": "Thierry", "initials": "T", "orcid": "0000-0001-9174-8599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09542eee2b7748769298e9d4fcdc5a22.json"}}, {"family": "Siesj\u00f6", "given": "Peter", "initials": "P"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI", "orcid": "0000-0003-1277-812X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e63aa6bb0fba481abeb58c2f1568b3c9.json"}}, {"family": "Kool", "given": "Marcel", "initials": "M", "orcid": "0000-0002-6557-5468", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da81ade40cfb45329b5ef3a190834913.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4.json"}}, {"family": "Darabi", "given": "Anna", "initials": "A", "orcid": "0000-0003-4326-8149", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb9f19a0c8694ee79ca515a79976d146.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e673fa8c86348fb8c1a2ae34ba7ba9a.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8825c33511418a83eceffdb530dadb.json"}}, {"family": "Wilhelm", "given": "Margareta", "initials": "M", "orcid": "0000-0002-0516-9724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b22feedd1d3c464ba7d8f6635fb00826.json"}}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "117", "issue": "33", "pages": "20127-20138", "issn-l": "0027-8424"}, "abstract": "Medulloblastoma is the most common malignant brain tumor in children. Here we describe a medulloblastoma model using Induced pluripotent stem (iPS) cell-derived human neuroepithelial stem (NES) cells generated from a Gorlin syndrome patient carrying a germline mutation in the sonic hedgehog (SHH) receptor PTCH1. We found that Gorlin NES cells formed tumors in mouse cerebellum mimicking human medulloblastoma. Retransplantation of tumor-isolated NES (tNES) cells resulted in accelerated tumor formation, cells with reduced growth factor dependency, enhanced neurosphere formation in vitro, and increased sensitivity to Vismodegib. Using our model, we identified LGALS1 to be a GLI target gene that is up-regulated in both Gorlin tNES cells and SHH-subgroup of medulloblastoma patients. Taken together, we demonstrate that NES cells derived from Gorlin patients can be used as a resource to model medulloblastoma initiation and progression and to identify putative targets.", "doi": "10.1073/pnas.1920521117", "pmid": "32747535", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7443968"}, {"db": "pii", "key": "1920521117"}], "notes": [], "created": "2026-08-20T09:30:35.661Z", "modified": "2026-08-20T09:30:36.075Z"}]}