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"https://publications-affiliated.scilifelab.se/researcher/2447e7e528854175bc2211b320c926c0.json"}}, {"family": "Marques Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Farh", "given": "Kyle Kai-How", "initials": "KK", "orcid": "0000-0001-6947-8537", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e26652330e794c388fa38913fbd17703.json"}}], "type": "comparative study", "published": "2024-01-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "625", "issue": "7996", "pages": "735-742", "issn-l": "0028-0836"}, "abstract": "Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.", "doi": "10.1038/s41586-023-06798-8", "pmid": "38030727", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10808062"}, {"db": "pii", "key": "10.1038/s41586-023-06798-8"}], "notes": [], "created": "2026-09-23T07:36:26.885Z", "modified": "2026-09-23T07:36:28.837Z"}, {"entity": "publication", "iuid": "b9fd8cd4df2f4cfd90ea1c40bf40619e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b9fd8cd4df2f4cfd90ea1c40bf40619e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b9fd8cd4df2f4cfd90ea1c40bf40619e"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/997ea196d4ae4c9790a715246dbfac82.json"}}, {"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fc8b6ee363a4ccaaea909392715888a.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acaddec22cd64c8aaec92764cd4adf08.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9785e94b95a3466dbb70ad8eb9b34ccd.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5766930b7e3946e5a3f2e268605ab97b.json"}}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c59458e7834499cbe990b1f9b83236c.json"}}, {"family": "Hindle", "given": "Allyson G", "initials": "AG", "orcid": "0000-0002-1983-9573", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49459b37810943aca91c847060596160.json"}}, {"family": "Andrews", "given": "Gregory", "initials": "G", "orcid": "0000-0002-9880-3965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b10e5f60ff3241758e65b9dca69fad7b.json"}}, {"family": "Armstrong", "given": "Joel C", "initials": "JC"}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}}, {"family": "Breit", "given": "Ana M", "initials": "AM", "orcid": "0000-0002-4990-3353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db59adc2e4054528823c09df71a8c299.json"}}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7999277bf08b4dbdbcc7d5e78cafcb00.json"}}, {"family": "Fanter", "given": "Cornelia", "initials": "C", "orcid": "0000-0002-4591-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e011e81556cb445fb045b25f9c0cf7dc.json"}}, {"family": "Foley", "given": "Nicole M", "initials": "NM", "orcid": "0000-0002-8169-9436", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/109dac01ce9c443cbbe73e3d0d4f0f2f.json"}}, {"family": "Goodman", "given": "Daniel B", 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{"family": "Johnson", "given": "Jeremy", "initials": "J", "orcid": "0000-0001-8548-5972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ec69a3f2cdf4e3bbe0fb10a53c45fea.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cef7ddc40d8f47468f3f3dec3caa5de3.json"}}, {"family": "Lawler", "given": "Alyssa J", "initials": "AJ", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3c0a5c01064277918e610c2e6f97d7.json"}}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD", "orcid": "0000-0002-4803-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01f46abb4cbc4f269440556154454ebb.json"}}, {"family": "Morrill", "given": "Kathleen M", "initials": "KM", "orcid": "0000-0002-9139-453X", "researcher": {"href": 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E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7f399939ae14daa8c0bd9bf5b92a896.json"}}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9386c16bd7e14ddca60e03e06f6808fe.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/073a9fab924c4e96973f1e23accaa7ae.json"}}, {"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b080282d4674df1bde072812bf448be.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": 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"orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b1fba9de46a4c8c8cbbbec685a9b94c.json"}}, {"family": "Nweeia", "given": "Martin", "initials": "M", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6848f42df6b146df8fd953c169193eb4.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f15a636469944ddb56489a74a75591b.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddf0080c6ee44cbe830114f0ab126884.json"}}, {"family": "Springer", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-7335-6946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93985cf0515345b8b302228258be970e.json"}}, {"family": "Teeling", "given": "Emma C", "initials": "EC", "orcid": "0000-0002-3309-1346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28069443db794cb596e58aea060d9dea.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22242b8810024fa6b7c098ced475db12.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Levesque", "given": "Danielle L", "initials": "DL", "orcid": "0000-0003-0132-8094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/291c0db9f1014708bfe1c52a946e1df7.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a71bcbcd8a6437ea7c32ce512ebd38c.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8360a54a1b447d0b67d85b3f1e40b5a.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c916e24b35f2459480cf87e27bb21ee1.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d080bc9bff548958f0c161612cdc4cf.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6392a5497414b98999823cbafd67d4b.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbc58d9ceb8d490baab61cb6002cecbe.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7c2be6e32147d19f03c7ff88fb3f80.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn3943", "issn-l": "0036-8075"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2026-09-23T06:39:33.319Z", "modified": "2026-09-23T06:39:34.893Z"}]}