Transcriptional activity and strain-specific history of mouse pseudogenes

• Published in: Nature communications 2020-07, Vol.11 (1), p.3695-3695, Article 3695
• Main Authors: Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark
• Format: Article
• Language: English
• Subjects: 45/91; 631/114/2401; 631/114/2785; 631/136/334/1874/345; 631/208/212/2304; 64/60; Age composition; Animals; Annotations; Conserved Sequence - genetics; Evolution; Evolution, Molecular; Evolutionary genetics; Gene Ontology; Genome; Genomes; Glyceraldehyde-3-phosphate dehydrogenase; Humanities and Social Sciences; Humans; Inbreeding; Markers; Mice, Inbred C57BL; Molecular Sequence Annotation; multidisciplinary; Pseudogenes; Pseudogenes - genetics; Ribosomal proteins; Rodents; Science; Science (multidisciplinary); Species Specificity; Transcription; Transcription, Genetic
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-17157-w

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.