{"entity": "researcher", "timestamp": "2026-08-15T06:41:58.730Z", "family": "Horvath", "given": "Vivien", "initials": "V", "orcid": "0000-0001-6536-1710", "affiliations": ["Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7be63bec9f4a4bf2a0fa907973cef28d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7be63bec9f4a4bf2a0fa907973cef28d"}}, "publications": [{"entity": "publication", "iuid": "744a6ad4f05545bea2cb39642ffe1e88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/744a6ad4f05545bea2cb39642ffe1e88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/744a6ad4f05545bea2cb39642ffe1e88"}}, "title": "Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.", "authors": [{"family": "Horv\u00e1th", "given": "Vivien", "initials": "V", "orcid": "0000-0001-6536-1710", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be63bec9f4a4bf2a0fa907973cef28d.json"}}, {"family": "Garza", "given": "Raquel", "initials": "R"}, {"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME"}, {"family": "Johansson", "given": "Pia A", "initials": "PA"}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Christoforidou", "given": "Georgia", "initials": "G"}, {"family": "Karlsson", "given": "Ofelia", "initials": "O"}, {"family": "Castilla Vallmanya", "given": "Laura", "initials": "L"}, {"family": "Koutounidou", "given": "Symela", "initials": "S", "orcid": "0009-0003-6710-8374", "researcher": {"href": "https://publications.scilifelab.se/researcher/bacb26c356f74e6ba8da4d55b7dc4b15.json"}}, {"family": "Gerdes", "given": "Patricia", "initials": "P", "orcid": "0000-0002-1148-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8571bfad113498c8fdb09fb74d7b2bd.json"}}, {"family": "Pandiloski", "given": "Ninoslav", "initials": "N"}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nat. Struct. Mol. Biol.", "issn": "1545-9985", "volume": "31", "issue": "10", "pages": "1543-1556", "issn-l": "1545-9985"}, "abstract": "SVA (SINE (short interspersed nuclear element)-VNTR (variable number of tandem repeats)-Alu) retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized and how their regulatory impact is constrained by an innate epigenetic defense system.", "doi": "10.1038/s41594-024-01320-8", "pmid": "38834915", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11479940"}, {"db": "pii", "key": "10.1038/s41594-024-01320-8"}], "notes": [], "created": "2024-09-03T12:22:35.346Z", "modified": "2024-11-15T06:29:49.161Z"}, {"entity": "publication", "iuid": "49731da5fcb34c8ea7886628fc04fb77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49731da5fcb34c8ea7886628fc04fb77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49731da5fcb34c8ea7886628fc04fb77"}}, "title": "LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification.", "authors": [{"family": "Garza", "given": "Raquel", "initials": "R", "orcid": "0000-0002-2524-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d53399af304283ba62e0646acdc612.json"}}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM", "orcid": "0000-0002-6158-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2c36afdcd3147f39ad6e34623dbec6c.json"}}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Gerdes", "given": "Patricia", "initials": "P", "orcid": "0000-0002-1148-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8571bfad113498c8fdb09fb74d7b2bd.json"}}, {"family": "Vinod", "given": "Meghna", "initials": "M", "orcid": "0009-0008-9057-6834", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9ee947419d440f82ea756abb28d7f9.json"}}, {"family": "Hsieh", "given": "PingHsun", "initials": "P", "orcid": "0000-0001-8294-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/00e1f1a68324444ea4e89ec62fc12d64.json"}}, {"family": "Karlsson", "given": "Ofelia", "initials": "O"}, {"family": "Horvath", "given": "Vivien", "initials": "V", "orcid": "0000-0001-6536-1710", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be63bec9f4a4bf2a0fa907973cef28d.json"}}, {"family": "Johansson", "given": "Pia A", "initials": "PA", "orcid": "0000-0002-6938-4060", "researcher": {"href": "https://publications.scilifelab.se/researcher/28206ae896f34a2c85c2ed863d4eb53e.json"}}, {"family": "Pandiloski", "given": "Ninoslav", "initials": "N", "orcid": "0000-0002-1204-5359", "researcher": {"href": "https://publications.scilifelab.se/researcher/156ba4836c234d739d10e0da00acce9b.json"}}, {"family": "Matas-Fuentes", "given": "Jon", "initials": "J", "orcid": "0009-0000-9253-1172", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a4d7313057548238c742aefc9c07ca8.json"}}, {"family": "Quaegebeur", "given": "Annelies", "initials": "A", "orcid": "0000-0001-5357-9341", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2f37a3920374d37a1d5508b580ddac2.json"}}, {"family": "Kouli", "given": "Antonina", "initials": "A", "orcid": "0000-0001-6553-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/6894568633154da5aad7f93413297f43.json"}}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME", "orcid": "0000-0002-1184-6269", "researcher": {"href": "https://publications.scilifelab.se/researcher/73ddc70ea52e4bfc82f97a3fc35c09cd.json"}}, {"family": "Monni", "given": "Emanuela", "initials": "E", "orcid": "0000-0003-0083-1050", "researcher": {"href": "https://publications.scilifelab.se/researcher/3becd99e5a7d4d5e8a4d893045dcb590.json"}}, {"family": "Englund", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-2708-2443", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c98fa2b2e7e4e318cd00eb1e8e3ac7a.json"}}, {"family": "Eichler", "given": "Evan E", "initials": "EE", "orcid": "0000-0002-8246-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/43901cc9fc3b4f5c9a18260e36558eb9.json"}}, {"family": "Gale Hammell", "given": "Molly", "initials": "M", "orcid": "0000-0003-0405-8392", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbbae421ea14d5c983755df8f519930.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Kokaia", "given": "Zaal", "initials": "Z"}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "44", "pages": "eadh9543", "issn-l": "2375-2548"}, "abstract": "The genetic mechanisms underlying the expansion in size and complexity of the human brain remain poorly understood. Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. Using multiomics profiling, we here demonstrate that L1 promoters are dynamically active in the developing and the adult human brain. L1s generate hundreds of developmentally regulated and cell type-specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPR interference silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.", "doi": "10.1126/sciadv.adh9543", "pmid": "37910626", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10619931"}], "notes": [], "created": "2023-11-02T13:41:55.614Z", "modified": "2023-11-21T18:50:22.968Z"}]}