The functional and evolutionary impacts of human-specific deletions in conserved elements

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Xue, James R.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.;Harvard Univ, Ctr Syst Biol, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA. (author)

The functional and evolutionary impacts of human-specific deletions in conserved elements

Article/chapterEnglish2023

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American Association for the Advancement of Science (AAAS),2023
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LIBRIS-ID:oai:DiVA.org:uu-505570
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-505570URI
https://doi.org/10.1126/science.abn2253DOI

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Language:English
Summary in:English

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

Notes

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Subject headings and genre

MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Medicinsk genetik hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Medical Genetics hsv//eng
NATURVETENSKAP Biologi Genetik hsv//swe
NATURAL SCIENCES Biological Sciences Genetics hsv//eng
NATURVETENSKAP Biologi Utvecklingsbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Developmental Biology hsv//eng

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Mackay-Smith, AvaYale Sch Med, Dept Genet, New Haven, CT 06510 USA. (author)
Mouri, KousukeJackson Lab, Bar Harbor, ME USA. (author)
Garcia, Meilin FernandezYale Univ, Dept Psychiat, New Haven, CT USA. (author)
Dong, Michael X.Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)micdo164 (author)
Akers, Jared F.Yale Sch Med, Dept Genet, New Haven, CT 06510 USA. (author)
Noble, MarkYale Sch Med, Dept Genet, New Haven, CT 06510 USA. (author)
Li, XueBroad Inst MIT & Harvard, Cambridge, MA 02142 USA.;UMass Chan Med Sch, Program Bioinformat & Integrat Biol, Worcester, MA USA.;UMass Chan Med Sch, Program Mol Med, Worcester, MA USA. (author)
Lindblad-Toh, KerstinUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.(Swepub:uu)kerli865 (author)
Karlsson, Elinor K.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.;UMass Chan Med Sch, Program Bioinformat & Integrat Biol, Worcester, MA USA.;UMass Chan Med Sch, Program Mol Med, Worcester, MA USA. (author)
Noonan, James P.Yale Sch Med, Dept Genet, New Haven, CT 06510 USA.;Yale Sch Med, Dept Neurosci, New Haven, CT USA.;Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT USA. (author)
Capellini, Terence D.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.;Harvard Univ, Human Evolutionary Biol, Cambridge, MA USA. (author)
Brennand, Kristen J.Yale Sch Med, Dept Genet, New Haven, CT 06510 USA.;Yale Univ, Dept Psychiat, New Haven, CT USA. (author)
Tewhey, RyanJackson Lab, Bar Harbor, ME USA.;Univ Maine, Grad Sch Biomed Sci & Engn, Orono, ME USA.;Tufts Univ, Grad Sch Biomed Sci, Sch Med, Boston, MA USA. (author)
Sabeti, Pardis C.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.;Harvard Univ, Ctr Syst Biol, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.;Howard Hughes Med Inst, Chevy Chase, MD USA.;Harvard TH Chan Sch Publ Hlth, Dept Immunol & Infect Dis, Boston, MA USA. (author)
Reilly, Steven K.Yale Sch Med, Dept Genet, New Haven, CT 06510 USA. (author)
Consortium, Zoonomia (author)
Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.;Harvard Univ, Ctr Syst Biol, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.Yale Sch Med, Dept Genet, New Haven, CT 06510 USA. (creator_code:org_t)

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In:Science: American Association for the Advancement of Science (AAAS)380:66430036-80751095-9203

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By the author/editor: Xue, James R.; Mackay-Smith, Av ...; Mouri, Kousuke; Garcia, Meilin F ...; Dong, Michael X.; Akers, Jared F.; show more...; Noble, Mark; Li, Xue; Lindblad-Toh, Ke ...; Karlsson, Elinor ...; Noonan, James P.; Capellini, Teren ...; Brennand, Kriste ...; Tewhey, Ryan; Sabeti, Pardis C ...; Reilly, Steven K ...; Consortium, Zoon ...; show less...

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MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Medical Genetics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Genetics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Developmental Bi ...

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By the university: Uppsala University

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