1. Transcriptional activity and strain-specific history of mouse pseudogenes
- Author
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Jennifer Harrow, Duncan T. Odom, David Thybert, Paul Flicek, Thomas M. Keane, Adam Frankish, Ian T. Fiddes, Cristina Sisu, Mark Gerstein, Paul R. Muir, Tim Hubbard, Mark Diekhans, Sisu, Cristina [0000-0001-9371-0797], Diekhans, Mark [0000-0002-0430-0989], Odom, Duncan T. [0000-0001-6201-5599], Flicek, Paul [0000-0002-3897-7955], Keane, Thomas M. [0000-0001-7532-6898], Hubbard, Tim [0000-0002-1767-9318], Gerstein, Mark [0000-0002-9746-3719], Apollo - University of Cambridge Repository, Odom, Duncan T [0000-0001-6201-5599], and Keane, Thomas M [0000-0001-7532-6898]
- Subjects
0301 basic medicine ,Mouse ,Transcription, Genetic ,Pseudogene ,Science ,General Physics and Astronomy ,Biology ,631/208/212/2304 ,Genome informatics ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,Ribosomal protein ,631/136/334/1874/345 ,Animals ,Humans ,lcsh:Science ,Gene ,Conserved Sequence ,Genetics ,45/91 ,Transcriptional activity ,Multidisciplinary ,Repertoire ,Strain (biology) ,article ,Molecular Sequence Annotation ,General Chemistry ,Genome evolution ,Mice, Inbred C57BL ,030104 developmental biology ,Gene Ontology ,631/114/2401 ,631/114/2785 ,lcsh:Q ,Data integration ,64/60 ,030217 neurology & neurosurgery ,Pseudogenes ,Reference genome - 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., Pseudogenes are key markers of genome remodelling processes. Here the authors present genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains, update human pseudogene annotations, and characterise the transcription and evolution of mouse pseudogenes.
- Published
- 2020
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