Identification of constrained sequence elements across 239 primate genomes

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Fältnamn	Indikatorer	Metadata
000		06920naa a2201417 4500
001		oai:DiVA.org:uu-520342
003		SwePub
008		240112s2024 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5203422 URI
024	7	a https://doi.org/10.1038/s41586-023-06798-82 DOI
040		a (SwePub)uu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Kuderna, Lukas F. K.4 aut
245	1 0	a Identification of constrained sequence elements across 239 primate genomes
264	1	b Springer Nature,c 2024
338		a electronic2 rdacarrier
520		a 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 genome3,4,5,6,7,8,9. 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.
650	7	a NATURVETENSKAPx Biologix Genetik0 (SwePub)106092 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciencesx Genetics0 (SwePub)106092 hsv//eng
650	7	a NATURVETENSKAPx Biologix Evolutionsbiologi0 (SwePub)106152 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciencesx Evolutionary Biology0 (SwePub)106152 hsv//eng
700	1	a Ulirsch, Jacob C.4 aut
700	1	a Rashid, Sabrina4 aut
700	1	a Ameen, Mohamed4 aut
700	1	a Sundaram, Laksshman4 aut
700	1	a Hickey, Glenn4 aut
700	1	a Cox, Anthony J.4 aut
700	1	a Gao, Hong4 aut
700	1	a Kumar, Arvind4 aut
700	1	a Aguet, Francois4 aut
700	1	a Christmas, Matthew J.u Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab4 aut0 (Swepub:uu)match108
700	1	a Clawson, Hiram4 aut
700	1	a Haeussler, Maximilian4 aut
700	1	a Janiak, Mareike C.4 aut
700	1	a Kuhlwilm, Martin4 aut
700	1	a Orkin, Joseph D.4 aut
700	1	a Bataillon, Thomas4 aut
700	1	a Manu, Shivakumara4 aut
700	1	a Valenzuela, Alejandro4 aut
700	1	a Bergman, Juraj4 aut
700	1	a Rouselle, Marjolaine4 aut
700	1	a Silva, Felipe Ennes4 aut
700	1	a Agueda, Lidia4 aut
700	1	a Blanc, Julie4 aut
700	1	a Gut, Marta4 aut
700	1	a de Vries, Dorien4 aut
700	1	a Goodhead, Ian4 aut
700	1	a Harris, R. Alan4 aut
700	1	a Raveendran, Muthuswamy4 aut
700	1	a Jensen, Axelu Uppsala universitet,Zooekologi4 aut0 (Swepub:uu)axeje389
700	1	a Chuma, Idriss S.4 aut
700	1	a Horvath, Julie E.4 aut
700	1	a Hvilsom, Christina4 aut
700	1	a Juan, David4 aut
700	1	a Frandsen, Peter4 aut
700	1	a Schraiber, Joshua G.4 aut
700	1	a de Melo, Fabiano R.4 aut
700	1	a Bertuol, Fabrício4 aut
700	1	a Byrne, Hazel4 aut
700	1	a Sampaio, Iracilda4 aut
700	1	a Farias, Izeni4 aut
700	1	a Valsecchi, João4 aut
700	1	a Messias, Malu4 aut
700	1	a da Silva, Maria N. F.4 aut
700	1	a Trivedi, Mihir4 aut
700	1	a Rossi, Rogerio4 aut
700	1	a Hrbek, Tomas4 aut
700	1	a Andriaholinirina, Nicole4 aut
700	1	a Rabarivola, Clément J.4 aut
700	1	a Zaramody, Alphonse4 aut
700	1	a Jolly, Clifford J.4 aut
700	1	a Phillips-Conroy, Jane4 aut
700	1	a Wilkerson, Gregory4 aut
700	1	a Abee, Christian4 aut
700	1	a Simmons, Joe H.4 aut
700	1	a Fernandez-Duque, Eduardo4 aut
700	1	a Kanthaswamy, Sree4 aut
700	1	a Shiferaw, Fekadu4 aut
700	1	a Wu, Dongdong4 aut
700	1	a Zhou, Long4 aut
700	1	a Shao, Yong4 aut
700	1	a Zhang, Guojie4 aut
700	1	a Keyyu, Julius D.4 aut
700	1	a Knauf, Sascha4 aut
700	1	a Le, Minh D.4 aut
700	1	a Lizano, Esther4 aut
700	1	a Merker, Stefan4 aut
700	1	a Navarro, Arcadi4 aut
700	1	a Nadler, Tilo4 aut
700	1	a Chuen Khor, Chiea4 aut
700	1	a Lee, Jessica4 aut
700	1	a Tan, Patrick4 aut
700	1	a Khong Lim, Weng4 aut
700	1	a Kitchener, Andrew C.4 aut
700	1	a Zinner, Dietmar4 aut
700	1	a Gut, Ivo4 aut
700	1	a Melin, Amanda D.4 aut
700	1	a Guschanski, Katerina,c Dr.d 1978-u Uppsala universitet,Zooekologi,Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK4 aut0 (Swepub:uu)katgu490
700	1	a Heide Schierup, Mikkel4 aut
700	1	a Beck, Robin M. D.4 aut
700	1	a Karakikes, Ioannis4 aut
700	1	a Wang, Kevin C.4 aut
700	1	a Umapathy, Govindhaswamy4 aut
700	1	a Roos, Christian4 aut
700	1	a Boubli, Jean P.4 aut
700	1	a Siepel, Adam4 aut
700	1	a Kundaje, Anshul4 aut
700	1	a Paten, Benedict4 aut
700	1	a Lindblad-Toh, Kerstinu Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Broad Institute of MIT and Harvard, Cambridge, MA, USA4 aut0 (Swepub:uu)kerli865
700	1	a Rogers, Jeffrey4 aut
700	1	a Marques Bonet, Tomas4 aut
700	1	a Kai-How Farh, Kyle4 aut
710	2	a Uppsala universitetb Institutionen för medicinsk biokemi och mikrobiologi4 org
773	0	t Natured : Springer Natureg 625:7996, s. 735-742q 625:7996<735-742x 0028-0836x 1476-4687
856	4	u https://doi.org/10.1038/s41586-023-06798-8y Fulltext
856	4	u https://uu.diva-portal.org/smash/get/diva2:1826846/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-520342
856	4 8	u https://doi.org/10.1038/s41586-023-06798-8

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Av författaren/redakt...: Kuderna, Lukas F ...; Ulirsch, Jacob C ...; Rashid, Sabrina; Ameen, Mohamed; Sundaram, Lakssh ...; Hickey, Glenn; visa fler...; Cox, Anthony J.; Gao, Hong; Kumar, Arvind; Aguet, Francois; Christmas, Matth ...; Clawson, Hiram; Haeussler, Maxim ...; Janiak, Mareike ...; Kuhlwilm, Martin; Orkin, Joseph D.; Bataillon, Thoma ...; Manu, Shivakumar ...; Valenzuela, Alej ...; Bergman, Juraj; Rouselle, Marjol ...; Silva, Felipe En ...; Agueda, Lidia; Blanc, Julie; Gut, Marta; de Vries, Dorien; Goodhead, Ian; Harris, R. Alan; Raveendran, Muth ...; Jensen, Axel; Chuma, Idriss S.; Horvath, Julie E ...; Hvilsom, Christi ...; Juan, David; Frandsen, Peter; Schraiber, Joshu ...; de Melo, Fabiano ...; Bertuol, Fabríci ...; Byrne, Hazel; Sampaio, Iracild ...; Farias, Izeni; Valsecchi, João; Messias, Malu; da Silva, Maria ...; Trivedi, Mihir; Rossi, Rogerio; Hrbek, Tomas; Andriaholinirina ...; Rabarivola, Clém ...; Zaramody, Alphon ...; Jolly, Clifford ...; Phillips-Conroy, ...; Wilkerson, Grego ...; Abee, Christian; Simmons, Joe H.; Fernandez-Duque, ...; Kanthaswamy, Sre ...; Shiferaw, Fekadu; Wu, Dongdong; Zhou, Long; Shao, Yong; Zhang, Guojie; Keyyu, Julius D.; Knauf, Sascha; Le, Minh D.; Lizano, Esther; Merker, Stefan; Navarro, Arcadi; Nadler, Tilo; Chuen Khor, Chie ...; Lee, Jessica; Tan, Patrick; Khong Lim, Weng; Kitchener, Andre ...; Zinner, Dietmar; Gut, Ivo; Melin, Amanda D.; Guschanski, Kate ...; Heide Schierup, ...; Beck, Robin M. D ...; Karakikes, Ioann ...; Wang, Kevin C.; Umapathy, Govind ...; Roos, Christian; Boubli, Jean P.; Siepel, Adam; Kundaje, Anshul; Paten, Benedict; Lindblad-Toh, Ke ...; Rogers, Jeffrey; Marques Bonet, T ...; Kai-How Farh, Ky ...; visa färre...

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