Transcriptional activity and strain-specific history of mouse pseudogenes

Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes, Mark Diekhans, David Thybert, Duncan T. Odom, Paul Flicek, Thomas M. Keane, Tim Hubbard, Jennifer Harrow and Mark Gerstein ()
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Cristina Sisu: Yale University
Paul Muir: 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
Duncan T. Odom: University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way
Paul Flicek: European Bioinformatics Institute, Wellcome 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

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17157-w

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