An evolutionary driver of interspersed segmental duplications in primates View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-08-10

AUTHORS

Stuart Cantsilieris, Susan M. Sunkin, Matthew E. Johnson, Fabio Anaclerio, John Huddleston, Carl Baker, Max L. Dougherty, Jason G. Underwood, Arvis Sulovari, PingHsun Hsieh, Yafei Mao, Claudia Rita Catacchio, Maika Malig, AnneMarie E. Welch, Melanie Sorensen, Katherine M. Munson, Weihong Jiang, Santhosh Girirajan, Mario Ventura, Bruce T. Lamb, Ronald A. Conlon, Evan E. Eichler

ABSTRACT

BackgroundThe complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human–ape gene families, nuclear pore interacting protein (NPIP).ResultsComparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis.ConclusionsLCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution. More... »

PAGES

202

References to SciGraph publications

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  • Journal

    TITLE

    Genome Biology

    ISSUE

    1

    VOLUME

    21

    Author Affiliations

  • Present Address: Centre for Eye Research Australia, Department of Surgery (Ophthalmology), University of Melbourne, Royal Victorian Eye and Ear Hospital, 3002, East Melbourne, VIC, Australia
  • Allen Institute for Brain Science, Seattle, WA, USA
  • Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, 19104, Philadelphia, PA, USA
  • Department of Biology-Genetics, University of Bari, Bari, Italy
  • Molecular and Cellular Biology Program, University of Washington, 98195, Seattle, WA, USA
  • Department of Genome Sciences, University of Washington School of Medicine, 98195, Seattle, WA, USA
  • Pacific Biosciences (PacBio) of California, Incorporated, 94025, Menlo Park, CA, USA
  • Present Address: Integrative Genetics and Genomics Graduate Group, University of California, 95616, Davis, CA, USA
  • Present Address: Brain and Mitochondrial Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
  • Case Transgenic and Targeting Facility, Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, 44106, Cleveland, OH, USA
  • Department of Biochemistry and Molecular Biology, Department of Anthropology, Pennsylvania State University, 16802, University Park, PA, USA
  • Stark Neurosciences Research Institute, Indiana University School of Medicine, 46202, Indianapolis, IN, USA
  • Howard Hughes Medical Institute, University of Washington School of Medicine, 3720 15th Ave NE, S413C, Box 355065, 98195-5065, Seattle, WA, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-020-02074-4

    DOI

    http://dx.doi.org/10.1186/s13059-020-02074-4

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1130018562

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/32778141


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