{"entity": "researcher", "timestamp": "2026-08-20T21:27:26.891Z", "family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "affiliations": ["Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.", "Science for Life Laboratory, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313"}}, "publications": [{"entity": "publication", "iuid": "0c50e62c624b482caae9dbf20827e59d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0c50e62c624b482caae9dbf20827e59d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0c50e62c624b482caae9dbf20827e59d"}}, "title": "Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.", "authors": [{"family": "Baranasic", "given": "Damir", "initials": "D", "orcid": "0000-0001-5948-0932", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/032c518e82dc4080a500eea5b696a475.json"}}, {"family": "H\u00f6rtenhuber", "given": "Matthias", "initials": "M", "orcid": "0000-0002-5599-5565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5dde3aca93c41e697f9cf8a18af5afe.json"}}, {"family": "Balwierz", "given": "Piotr J", "initials": "PJ", "orcid": "0000-0002-1548-4605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/731810eb0c9844db907d4e24809ea98f.json"}}, {"family": "Zehnder", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4127-2673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02b1665e13434c4f90490593cea4688d.json"}}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK"}, {"family": "Nepal", "given": "Chirag", "initials": "C"}, {"family": "V\u00e1rnai", "given": "Csilla", "initials": "C", "orcid": "0000-0003-0048-9507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2e8ea006bf84f97bbad52b4319d6a8b.json"}}, {"family": "Hadzhiev", "given": "Yavor", "initials": "Y", "orcid": "0000-0002-1134-4904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f069867d6cbb42e68f4c29c3c9e73ffc.json"}}, {"family": "Jimenez-Gonzalez", "given": "Ada", "initials": "A", "orcid": "0000-0001-7702-6135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/290dada7ad2641168db7315df84a91db.json"}}, {"family": "Li", "given": "Nan", "initials": "N", "orcid": "0000-0002-8919-2357", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff03d99df8146f9a8495908283fb3a8.json"}}, {"family": "Wragg", "given": "Joseph", "initials": "J"}, {"family": "D'Orazio", "given": "Fabio M", "initials": "FM"}, {"family": "Relic", "given": "Dorde", "initials": "D", "orcid": "0000-0001-6237-3345", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bf5a9430ac84692acf72775bdeb44e7.json"}}, {"family": "Pachkov", "given": "Mikhail", "initials": "M", "orcid": "0000-0001-7616-6435", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/603e6a04cbf149dca698067a1648db10.json"}}, {"family": "D\u00edaz", "given": "Noelia", "initials": "N", "orcid": "0000-0002-0319-3448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ffc9927ea4e40e89a973b4e498f988b.json"}}, {"family": "Hern\u00e1ndez-Rodr\u00edguez", "given": "Benjam\u00edn", "initials": "B", "orcid": "0000-0002-5118-8715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d543e6cf9ab4991a74afc120cef56a3.json"}}, {"family": "Chen", "given": "Zelin", "initials": "Z", "orcid": "0000-0002-8376-7367", "researcher": {"href": 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"given": "Sepand", "initials": "S", "orcid": "0000-0003-4411-5646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78de22af4c894c14a31082e636172dfb.json"}}, {"family": "McGarvey", "given": "Alison C", "initials": "AC"}, {"family": "Kopp", "given": "Wolfgang", "initials": "W", "orcid": "0000-0003-0376-0032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9a5ee826c51434883da186d3d1c89fa.json"}}, {"family": "Chambers", "given": "Emily", "initials": "E", "orcid": "0000-0003-1252-8059", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3744971f82284319924bff22e14952c3.json"}}, {"family": "Wang", "given": "Dennis", "initials": "D", "orcid": "0000-0003-0068-1005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53edc20f0942483995fe67dcc1f45baa.json"}}, {"family": "Kim", "given": "Hyejeong R", "initials": "HR"}, {"family": "Acemel", "given": "Rafael D", "initials": "RD", "orcid": "0000-0003-4120-0140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9419f6ea5e2e481eb2feeca0749880f6.json"}}, {"family": "Naranjo", "given": "Silvia", "initials": "S", "orcid": "0000-0002-4529-3332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd126710f25e4a4db11ecbba215c2625.json"}}, {"family": "\u0141api\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-4892-976X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da9b0191dcd84e8c883c2b682abb3726.json"}}, {"family": "Chong", "given": "Vanessa", "initials": "V", "orcid": "0000-0002-2547-3694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6398524010dd4dcb93dc07f8296e0bbe.json"}}, {"family": "Mathavan", "given": "Sinnakaruppan", "initials": "S"}, {"family": "Peers", "given": "Bernard", "initials": "B"}, {"family": "Sauka-Spengler", "given": "Tatjana", "initials": "T", "orcid": "0000-0001-9289-0263", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2151b40b1ad04efbb610e92037b22ae5.json"}}, {"family": "Vingron", "given": "Martin", "initials": "M", "orcid": "0000-0002-1765-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a96205b7e4e74c00907ac3945f79333a.json"}}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}, {"family": "Ohler", "given": "Uwe", "initials": "U", "orcid": "0000-0002-0881-3116", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcaea462c0ed46268ae98098b67eb1d3.json"}}, {"family": "Lacadie", "given": "Scott Allen", "initials": "SA"}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68cb29ca7d284d7292a0793852d86598.json"}}, {"family": "Winata", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-7718-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62550bd4fe4848aaad75a93e2efd2655.json"}}, {"family": "van Eeden", "given": "Freek", "initials": "F", "orcid": "0000-0003-3483-8269", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10acaef0681a496c8e7c32a69ba23120.json"}}, {"family": "Vaquerizas", "given": "Juan M", "initials": "JM", "orcid": "0000-0002-6583-6541", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51ab063af8d2475a97ddbb518841865e.json"}}, {"family": "G\u00f3mez-Skarmeta", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0001-5125-4332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3759f22a40fb4e1091156e1184f6d97e.json"}}, {"family": "Onichtchouk", "given": "Daria", "initials": "D", "orcid": "0000-0001-6497-1445", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e8f702587c948fbb94123ad355f534b.json"}}, {"family": "Brown", "given": "Ben James", "initials": "BJ", "orcid": "0000-0002-5898-5848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cd670fd0b3c45f9a5ba05a562ce8744.json"}}, {"family": "Bogdanovic", "given": "Ozren", "initials": "O", "orcid": "0000-0001-5680-0056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fa7d945ca8843a1b0b462b3a6ed3cbf.json"}}, {"family": "van Nimwegen", "given": "Erik", "initials": "E", "orcid": "0000-0001-6338-1312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13de7adbce874eb9ab805197198d78e1.json"}}, {"family": "Westerfield", "given": "Monte", "initials": "M", "orcid": "0000-0003-1187-7839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eab74cd5a2c0406d8f5266b3708b624c.json"}}, {"family": "Wardle", "given": "Fiona C", "initials": "FC", "orcid": "0000-0001-5444-1889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cfeac2d939924d77bbcf7ff8e5479257.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}, {"family": "Lenhard", "given": "Boris", "initials": "B", "orcid": "0000-0002-1114-1509", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/938595001de64507a66e000512ce65cc.json"}}, {"family": "M\u00fcller", "given": "Ferenc", "initials": "F", "orcid": "0000-0002-0996-774X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a49e4212e5774247bb5d49bada60b8e5.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "54", "issue": "7", "pages": "1037-1050", "issn-l": "1061-4036"}, "abstract": "Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.", "doi": "10.1038/s41588-022-01089-w", "pmid": "35789323", "labels": [], "xrefs": [{"db": "mid", "key": "EMS144747"}, {"db": "pmc", "key": "PMC9279159"}, {"db": "pii", "key": "10.1038/s41588-022-01089-w"}], "notes": [], "created": "2026-08-20T08:59:56.776Z", "modified": "2026-08-20T08:59:58.224Z"}, {"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": "55cddf2e72f64458a6886bf7795c6217", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/55cddf2e72f64458a6886bf7795c6217.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/55cddf2e72f64458a6886bf7795c6217"}}, "title": "Sequence determinants of human gene regulatory elements.", "authors": [{"family": "Sahu", "given": "Biswajyoti", "initials": "B", "orcid": "0000-0001-6576-5440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8e3ffa4583845e79240284526722033.json"}}, {"family": "Hartonen", "given": "Tuomo", "initials": "T"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-9725-6907", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e5f7eadc49d4be4ab5f048cc421fb5f.json"}}, {"family": "Wei", "given": "Bei", "initials": "B"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Zhu", "given": "Fangjie", "initials": "F"}, {"family": "Kaasinen", "given": "Eevi", "initials": "E", "orcid": "0000-0002-1333-8049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f69778f4d2754fd0a6b603950c96fcab.json"}}, {"family": "Lidschreiber", "given": "Katja", "initials": "K", "orcid": "0000-0001-6319-1076", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e54e444599c409a83b56b454153d9bc.json"}}, {"family": "Lidschreiber", "given": "Michael", "initials": "M", "orcid": "0000-0002-6740-2755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10b20b1d5d95471489e71e62531e07b3.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}, {"family": "Cramer", "given": "Patrick", "initials": "P", "orcid": "0000-0001-5454-7755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fc67920867d466eb25758cdc13c2054.json"}}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/512ddc03d00c4e3984a44489be715610.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "54", "issue": "3", "pages": "283-294", "issn-l": "1061-4036"}, "abstract": "DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger sequence space than the human genome using massively parallel reporter assays (MPRAs). Machine learning models revealed that transcription factors (TFs) generally act in an additive manner with weak grammar and that most enhancers increase expression from a promoter by a mechanism that does not appear to involve specific TF-TF interactions. The enhancers themselves can be classified into three types: classical, closed chromatin and chromatin dependent. We also show that few TFs are strongly active in a cell, with most activities being similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening and enhancing, promoting and determining transcription start site (TSS) activity, consistent with the view that the TF binding motif is the key atomic unit of gene expression.", "doi": "10.1038/s41588-021-01009-4", "pmid": "35190730", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8920891"}, {"db": "pii", "key": "10.1038/s41588-021-01009-4"}], "notes": [], "created": "2026-08-20T08:59:54.664Z", "modified": "2026-08-20T08:59:54.963Z"}, {"entity": "publication", "iuid": "4f1217d2e2aa42c0ad7ecacc364c00ec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f1217d2e2aa42c0ad7ecacc364c00ec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f1217d2e2aa42c0ad7ecacc364c00ec"}}, "title": "Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish", "authors": [{"family": "Baranasic", "given": "Damir", "initials": "D", "orcid": "0000-0001-5948-0932", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/032c518e82dc4080a500eea5b696a475.json"}}, {"family": "H\u00f6rtenhuber", "given": "Matthias", "initials": "M", "orcid": "0000-0002-5599-5565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5dde3aca93c41e697f9cf8a18af5afe.json"}}, {"family": "Balwierz", "given": "Piotr", "initials": "P", "orcid": "0000-0002-1548-4605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/731810eb0c9844db907d4e24809ea98f.json"}}, {"family": "Zehnder", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4127-2673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02b1665e13434c4f90490593cea4688d.json"}}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK", "orcid": "0000-0002-9726-0399", 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"given": "Tuomo", "initials": "T"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Wei", "given": "Bei", "initials": "B"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Zhu", "given": "Fangjie", "initials": "F"}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "Lidschreiber", "given": "Katja", "initials": "K"}, {"family": "Lidschreiber", "given": "Michael", "initials": "M"}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}, {"family": "Cramer", "given": "Patrick", "initials": "P"}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0002-6851-9912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1373dc2dfe094f5f8f08ceb5e680d8ca.json"}}], "type": "posted-content", "published": "2021-03-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.03.18.435942", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:03:18.562Z", "modified": "2026-08-20T10:03:18.655Z"}, {"entity": "publication", "iuid": "66160c79e42a4166b013d4eef40ca15d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66160c79e42a4166b013d4eef40ca15d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66160c79e42a4166b013d4eef40ca15d"}}, "title": "Ten simple rules for annotating sequencing experiments.", "authors": [{"family": "Stevens", "given": "Irene", "initials": "I", "orcid": "0000-0003-3823-1499", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89f8823541844106b92311e5cd7ec22a.json"}}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK", "orcid": "0000-0002-9726-0399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65c7a0a3235f4a44b879d7b273a19daf.json"}}, {"family": "H\u00f6rtenhuber", "given": "Matthias", "initials": "M", "orcid": "0000-0002-5599-5565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5dde3aca93c41e697f9cf8a18af5afe.json"}}, {"family": "Meehan", "given": "Terrence F", "initials": "TF"}, {"family": "Rung", "given": "Johan", "initials": "J", "orcid": "0000-0001-5875-8429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c228edaa5b24d909714c4ea35a6bff8.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}], "type": "editorial", "published": "2020-10-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "16", "issue": "10", "pages": "e1008260", "issn-l": "1553-734X"}, "abstract": null, "doi": "10.1371/journal.pcbi.1008260", "pmid": "33017400", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7535046"}, {"db": "pii", "key": "PCOMPBIOL-D-20-00480"}], "notes": [], "created": "2026-08-20T12:42:55.292Z", "modified": "2026-08-20T12:42:55.396Z"}, {"entity": "publication", "iuid": "6fd33e86eb9d4788b90dee7f6fe58e7f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6fd33e86eb9d4788b90dee7f6fe58e7f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6fd33e86eb9d4788b90dee7f6fe58e7f"}}, "title": "A putative silencer variant in a spontaneous canine model of retinitis pigmentosa.", "authors": [{"family": "Kaukonen", "given": "Maria", "initials": "M", "orcid": "0000-0002-2146-4694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2afae3aaa8d244acbf8dc5388141bcb1.json"}}, {"family": "Quintero", "given": "Ileana B", "initials": "IB"}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK", "orcid": "0000-0002-9726-0399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65c7a0a3235f4a44b879d7b273a19daf.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1389bbb3ba141598a0a896b056dea89.json"}}, {"family": "Holopainen", "given": "Saila", "initials": "S", "orcid": "0000-0002-2448-7672", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c4cb476c0a540eb96e58ffb874bf15f.json"}}, {"family": "Wickstr\u00f6m", "given": "Kaisa", "initials": "K", "orcid": "0000-0003-4168-9951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc877dd4adf9486d8eb8bb1ba6e5eff8.json"}}, {"family": "Ky\u00f6stil\u00e4", "given": "Kaisa", "initials": "K"}, {"family": "Arumilli", "given": "Meharji", "initials": "M", "orcid": "0000-0003-4072-0996", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eefc37ebb7b841e497e93a14bd4b1fec.json"}}, {"family": "Jalom\u00e4ki", "given": "Sari", "initials": "S", "orcid": "0000-0003-0755-0948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c0ce8ddc53c342d69ae1c12550fa7cd0.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/779af7484e984ad6883a105caa008313.json"}}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eab428714c9f4f5eb0de63ffc7500f25.json"}}, {"family": "DoGA Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "16", "issue": "3", "pages": "e1008659", "issn-l": "1553-7390"}, "abstract": "Retinitis pigmentosa (RP) is the leading cause of blindness with nearly two million people affected worldwide. Many genes have been implicated in RP, yet in 30-80% of the RP patients the genetic cause remains unknown. A similar phenotype, progressive retinal atrophy (PRA), affects many dog breeds including the Miniature Schnauzer. We performed clinical, genetic and functional experiments to identify the genetic cause of PRA in the breed. The age of onset and pattern of disease progression suggested that at least two forms of PRA, types 1 and 2 respectively, affect the breed, which was confirmed by genome-wide association study that implicated two distinct genomic loci in chromosomes 15 and X, respectively. Whole-genome sequencing revealed a fully segregating recessive regulatory variant in type 1 PRA. The associated variant has a very recent origin based on haplotype analysis and lies within a regulatory site with the predicted binding site of HAND1::TCF3 transcription factor complex. Luciferase assays suggested that mutated regulatory sequence increases expression. Case-control retinal expression comparison of six best HAND1::TCF3 target genes were analyzed with quantitative reverse-transcriptase PCR assay and indicated overexpression of EDN2 and COL9A2 in the affected retina. Defects in both EDN2 and COL9A2 have been previously associated with retinal degeneration. In summary, our study describes two genetically different forms of PRA and identifies a fully penetrant variant in type 1 form with a possible regulatory effect. This would be among the first reports of a regulatory variant in retinal degeneration in any species, and establishes a new spontaneous dog model to improve our understanding of retinal biology and gene regulation while the affected breed will benefit from a reliable genetic testing.", "doi": "10.1371/journal.pgen.1008659", "pmid": "32150541", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7082071"}, {"db": "pii", "key": "PGENETICS-D-19-00950"}], "notes": [], "created": "2026-08-20T12:43:42.026Z", "modified": "2026-08-20T12:43:42.286Z"}]}