An evolutionary driver of interspersed segmental duplications in primates

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. LambRonald A. Conlon, Evan E. Eichler

Research output: Contribution to journalArticle

Abstract

Background: The 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). Results: Comparative 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. Conclusions: LCR16a 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.

Original languageEnglish (US)
Article number202
JournalGenome biology
Volume21
Issue number1
DOIs
StatePublished - Aug 10 2020

Keywords

  • Gene fusion
  • Genomic instability
  • LCR16a
  • Nuclear pore interacting protein
  • Segmental duplication

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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  • Cite this

    Cantsilieris, S., Sunkin, S. M., Johnson, M. E., Anaclerio, F., Huddleston, J., Baker, C., Dougherty, M. L., Underwood, J. G., Sulovari, A., Hsieh, P., Mao, Y., Catacchio, C. R., Malig, M., Welch, A. E., Sorensen, M., Munson, K. M., Jiang, W., Girirajan, S., Ventura, M., ... Eichler, E. E. (2020). An evolutionary driver of interspersed segmental duplications in primates. Genome biology, 21(1), [202]. https://doi.org/10.1186/s13059-020-02074-4