REGULATION OF GENE EXPRESSION IN TRIPLOID VERTEBRATES

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Allele-specific expression variation at different ploidy levels in Squalius alburnoides

Publication . Matos, Isa; Machado, Miguel P.; Schartl, Manfred; Coelho, Maria Manuela

Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.

2019Artigo científico

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Gene expression regulation in allopolyploid fish

Publication . Matos, Isa; Coelho, Maria Manuela; Schartl, Manfred

Plants, invertebrates and even lower vertebrates are known to deal with hybridization and polyploidy very successfully, surpassing the genetic constrains those phenomena bring. However, (allo)polyploidy in animals have been strongly neglected so, this matter remains largely unexplored. In that sense, the general goal of this thesis was to expand the existing limited knowledge on the topic, standing a significant step forward in the scarce information available on animal allopolyploid gene expression regulation. The inception of this work was a theory of occurrence of global dosage compensation by allele copy silencing in Squalius alburnoides complex. The elucidation of the inherent gene expression processes and mechanisms operating in S. alburnoides, and if they are a particular feature of this complex or have a more widespread occurrence among allopolyploids, were the main goals. The first step taken was the exclusion of ploidy mosaicism, a phenomenon here for the first time described to occur in S. alburnoides, as the source of the allele specific expression differences previously found. Despite it was corroborated that S. alburnoides triploids are affected by a significant down regulation of gene expression, that does not correspond to a genome wide exact functional diploidization. Instead, a certain level of flexibility of expression within a range of mRNA amounts per locus was observed. That feature might be a key point in the mechanisms that allow lower vertebrates to endure and maintain ploidy changes so effectively. The down regulation of gene expression in triploid S. alburnoides was also found to be not dependent of allele copy silencing, as previously speculated. Extreme homoeolog expression bias, comprehending the complete silencing of alleles, have been found to affect a significant percentage of genes in S. alburnoides, as in laboratory produced triploid hybrid Oryzias latipes. However, the incidence of the homoeolog expression bias was not significantly affected by the ploidy level of the individuals, and the allelic silencing rate was similar between diploids and triploids. Additionally, the hypothesis of a down regulation of gene expression mediated by massive methylation occurrence in triploid hybrid genomes was not sustained, neither for S. alburnoides nor for P. formosa.

2018Tese de doutoramento

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Entidade financiadora

Fundação para a Ciência e a Tecnologia

Programa de financiamento

PIDDAC

Número da atribuição

SFRH/BD/61217/2009