The genomic context of retrocopies increases their chance of functional relevancy in mammals

• Type: Article in International Scientific Journal
• Date: 2020

Authors

Machado, JP (Author) Other; Agostinho Antunes (Author) FCUP

Journal

Title: Genomics

Vol. 112

Pages: 2410-2417

ISSN: 0888-7543

Publisher: Elsevier

Indexing

ISI Web of Knowledge - 2 Citations

Scopus - 2 Citations

Other information

Authenticus ID: P-00R-QN0

DOI: 10.1016/j.ygeno.2020.01.013

Abstract (EN): Described as "junk" DNA, pseudogenes are dead structures of previously active genes present in genomes. Pseudogenes are categorized into two main classes: processed pseudogenes, formed through retrotransposition, and non-processed pseudogenes, typically originated from gene decay following duplication events. The term "processed pseudogene" has changed to "retrocopy" since they are likely to evolve new functional roles and became a retrogene. Here, we surveyed 38,080 retrocopies from chimpanzee, dog, human, mouse, and rat genomes to assess their potential adaptive value. The retrocopies inserted in the same chromosome of the parental gene have higher chances of remain potentially "active" (absence of premature stop codons and frameshifts) (similar to 26.1%), while those placed into a different chromosome have a twofold decrease chance of continuing potentially "active" (similar to 7.52%). The genomic context of their placement seems associated with their expression. Retrocopies placed in intragenic regions and the same sense of the "host" gene have higher chances of being expressed relative to other genomic contexts. The proximity of retrocopies to their parental gene is associated with a lower decay rate, and their location likely influence their expression. Thus, despite their unclear role, retrocopies are probably involved in adaptive processes. Our results evidence natural selection acting in retrocopies.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8