A Genome-Wide Landscape of Retrocopies in Primate Genomes

Autor(es)

Navarro, Fabio C. P. ^{[1, 2]} ; Galante, Pedro A. F. ^[1]

Afiliação do(s) autor(es)

^[1] Hosp Sirio Libanes, Ctr Mol Oncol, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Dept Bioquim, BR-05508 Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: GENOME BIOLOGY AND EVOLUTION; v. 7, n. 8, p. 2265-2275, AUG 2015.
• Citações Web of Science: 14

Resumo

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (similar to 7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (similar to 10,000) in Platyrrhini (NewWorld Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primatehistory, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. (AU)

• Processo FAPESP: 12/24731-1 - Retrocópias: origens, polimorfismos e variações somáticas
• Beneficiário: Pedro Alexandre Favoretto Galante
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores