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Transcriptional activity and strain-specific history of mouse pseudogenes

Author

Listed:
  • Cristina Sisu

    (Yale University
    Yale University
    Brunel University London)

  • Paul Muir

    (Yale University
    Yale University)

  • Adam Frankish

    (European Bioinformatics Institute, Wellcome Genome Campus)

  • Ian Fiddes

    (University of California)

  • Mark Diekhans

    (University of California)

  • David Thybert

    (European Bioinformatics Institute, Wellcome Genome Campus
    Earlham Institute, Norwich Research Park)

  • Duncan T. Odom

    (University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Paul Flicek

    (European Bioinformatics Institute, Wellcome Genome Campus
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Thomas M. Keane

    (European Bioinformatics Institute, Wellcome Genome Campus)

  • Tim Hubbard

    (King’s College London)

  • Jennifer Harrow

    (Elexir, Wellcome Trust Genome Campus)

  • Mark Gerstein

    (Yale University
    Yale University
    Yale University
    Yale University)

Abstract

Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes.

Suggested Citation

  • Cristina Sisu & Paul Muir & Adam Frankish & Ian Fiddes & Mark Diekhans & David Thybert & Duncan T. Odom & Paul Flicek & Thomas M. Keane & Tim Hubbard & Jennifer Harrow & Mark Gerstein, 2020. "Transcriptional activity and strain-specific history of mouse pseudogenes," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17157-w
    DOI: 10.1038/s41467-020-17157-w
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