{"entity": "researcher", "timestamp": "2026-08-15T06:53:04.521Z", "family": "Atacho", "given": "Diahann A M", "initials": "DAM", "orcid": "0000-0002-6158-0235", "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.", "Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d2c36afdcd3147f39ad6e34623dbec6c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d2c36afdcd3147f39ad6e34623dbec6c"}}, "publications": [{"entity": "publication", "iuid": "cacf484e41274db9a8d7ab5b3963dc8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cacf484e41274db9a8d7ab5b3963dc8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cacf484e41274db9a8d7ab5b3963dc8d"}}, "title": "The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1.", "authors": [{"family": "Gustavsson", "given": "Emil K", "initials": "EK", "orcid": "0000-0003-0541-7537", "researcher": {"href": "https://publications.scilifelab.se/researcher/996f67ab34fb486aa921970420315b08.json"}}, {"family": "Sethi", "given": "Siddharth", "initials": "S", "orcid": "0000-0002-4398-4295", "researcher": {"href": "https://publications.scilifelab.se/researcher/433a0df98347474897c6c63975206b58.json"}}, {"family": "Gao", "given": "Yujing", "initials": "Y", "orcid": "0000-0002-4542-7062", "researcher": {"href": "https://publications.scilifelab.se/researcher/213e239576ee4891adbc3a1971d29c7b.json"}}, {"family": "Brenton", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0002-2381-8484", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1aabde514394f66be925aa9aa10e25b.json"}}, {"family": "Garc\u00eda-Ruiz", "given": "Sonia", "initials": "S", "orcid": "0000-0003-4913-5312", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0e93d9df684439892ef30ff73200a2.json"}}, {"family": "Zhang", "given": "David", "initials": "D"}, {"family": "Garza", "given": "Raquel", "initials": "R", "orcid": "0000-0002-2524-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d53399af304283ba62e0646acdc612.json"}}, {"family": "Reynolds", "given": "Regina H", "initials": "RH", "orcid": "0000-0001-6470-7919", "researcher": {"href": "https://publications.scilifelab.se/researcher/4397a45fd4cb4ea7a2a1706a0411f0d4.json"}}, {"family": "Evans", "given": "James R", "initials": "JR", "orcid": "0000-0003-2923-281X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fbc42acb41341ebba1b572af6751786.json"}}, {"family": "Chen", "given": "Zhongbo", "initials": "Z", "orcid": "0000-0001-6668-7202", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e05d1f791410d933bca331a7309a3.json"}}, {"family": "Grant-Peters", "given": "Melissa", "initials": "M", "orcid": "0000-0003-0585-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ae1ca65912b4142ac5e8a55b0bfa936.json"}}, {"family": "Macpherson", "given": "Hannah", "initials": "H", "orcid": "0000-0002-9535-4025", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b53a05c7f194155bf828cfa1723d4dd.json"}}, {"family": "Montgomery", "given": "Kylie", "initials": "K", "orcid": "0000-0001-6090-0703", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc6e3ca875354f79a54971e5341235f4.json"}}, {"family": "Dore", "given": "Rhys", "initials": "R", "orcid": "0000-0001-8417-8743", "researcher": {"href": "https://publications.scilifelab.se/researcher/a11f7079ca7740029a876c2dd5260946.json"}}, {"family": "Wernick", "given": "Anna I", "initials": "AI", "orcid": "0000-0001-9048-9492", "researcher": {"href": "https://publications.scilifelab.se/researcher/09b297e297994740b74d583a37c74e43.json"}}, {"family": "Arber", "given": "Charles", "initials": "C", "orcid": "0000-0002-9743-8134", "researcher": {"href": "https://publications.scilifelab.se/researcher/29b0c152839b4115a6da93dcc1ffb835.json"}}, {"family": "Wray", "given": "Selina", "initials": "S"}, {"family": "Gandhi", "given": "Sonia", "initials": "S", "orcid": "0000-0003-4395-2661", "researcher": {"href": "https://publications.scilifelab.se/researcher/01493b3d90a244149225710c5f61d1ed.json"}}, {"family": "Esselborn", "given": "Julian", "initials": "J", "orcid": "0000-0002-3499-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/b856091feda54167848a30d759ad11ea.json"}}, {"family": "Blauwendraat", "given": "Cornelis", "initials": "C", "orcid": "0000-0001-9358-8111", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dd14eb697a94083a02bbc7d522ea87b.json"}}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM", "orcid": "0000-0002-6158-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2c36afdcd3147f39ad6e34623dbec6c.json"}}, {"family": "Kouli", "given": "Antonina", "initials": "A", "orcid": "0000-0001-6553-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/6894568633154da5aad7f93413297f43.json"}}, {"family": "Quaegebeur", "given": "Annelies", "initials": "A"}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Englund", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-2708-2443", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c98fa2b2e7e4e318cd00eb1e8e3ac7a.json"}}, {"family": "Platt", "given": "Frances", "initials": "F"}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}, {"family": "Wood", "given": "Nicholas W", "initials": "NW", "orcid": "0000-0002-9500-3348", "researcher": {"href": "https://publications.scilifelab.se/researcher/850e5336e5c946d29c3375d616a01836.json"}}, {"family": "Houlden", "given": "Henry", "initials": "H", "orcid": "0000-0002-2866-7777", "researcher": {"href": "https://publications.scilifelab.se/researcher/72a57dac09a341ffb23a2ceb9762e1e3.json"}}, {"family": "Saini", "given": "Harpreet", "initials": "H"}, {"family": "Bento", "given": "Carla F", "initials": "CF", "orcid": "0000-0001-8377-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e028035dc8245d9bc33274cd656358a.json"}}, {"family": "Hardy", "given": "John", "initials": "J", "orcid": "0000-0002-3122-0423", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa5b456a58b40a48d97f0be528c0855.json"}}, {"family": "Ryten", "given": "Mina", "initials": "M", "orcid": "0000-0001-9520-6957", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7e1cb1b3c640449ea0571c4b3a01ac.json"}}], "type": "journal article", "published": "2024-06-28", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "26", "pages": "eadk1296", "issn-l": "2375-2548"}, "abstract": "Mutations in GBA1 cause Gaucher disease and are the most important genetic risk factor for Parkinson's disease. However, analysis of transcription at this locus is complicated by its highly homologous pseudogene, GBAP1. We show that >50% of short RNA-sequencing reads mapping to GBA1 also map to GBAP1. Thus, we used long-read RNA sequencing in the human brain, which allowed us to accurately quantify expression from both GBA1 and GBAP1. We discovered significant differences in expression compared to short-read data and identify currently unannotated transcripts of both GBA1 and GBAP1. These included protein-coding transcripts from both genes that were translated in human brain, but without the known lysosomal function-yet accounting for almost a third of transcription. Analyzing brain-specific cell types using long-read and single-nucleus RNA sequencing revealed region-specific variations in transcript expression. Overall, these findings suggest nonlysosomal roles for GBA1 and GBAP1 with implications for our understanding of the role of GBA1 in health and disease.", "doi": "10.1126/sciadv.adk1296", "pmid": "38924406", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11204300"}], "notes": [], "created": "2024-11-15T06:28:56.936Z", "modified": "2024-11-15T06:28:59.191Z"}, {"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"}]}