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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Elurbe, Dei M ; Paranjpe, Sarita S ; Georgiou, Georgios ; van Kruijsbergen, Ila ; Bogdanovic, Ozren ; Gibeaux, Romain ; Heald, Rebecca ; Lister, Ryan ; Huynen, Martijn A ; van Heeringen, Simon J ; Veenstra, Gert Jan C

Genome Biology, 2017-10, Vol.18 (1), p.198-18, Article 198 [Periódico revisado por pares]

England: BioMed Central Ltd

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Título:
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Autor: Elurbe, Dei M ; Paranjpe, Sarita S ; Georgiou, Georgios ; van Kruijsbergen, Ila ; Bogdanovic, Ozren ; Gibeaux, Romain ; Heald, Rebecca ; Lister, Ryan ; Huynen, Martijn A ; van Heeringen, Simon J ; Veenstra, Gert Jan C
Assuntos: Animals ; Bioinformatics ; Chromatin - metabolism ; Chromosome Deletion ; Chromosomes ; Common plantanna ; Deoxyribonucleic acid ; DNA ; DNA methylation ; DNA Transposable Elements ; Embryos ; Enhancer Elements, Genetic ; Enhancers ; Epigenesis, Genetic ; Epigenetics ; Epigenomics ; Event-related potentials ; Evolution ; Gene duplication ; Gene Expression ; Genetic aspects ; Genetic engineering ; Genome ; Genome evolution ; Genomes ; Genomics ; Homologous recombination ; Hybridization ; Hybridization, Genetic ; Interspecific hybridization ; Life Sciences ; Morphology ; Physiological aspects ; Ploidy ; Pseudogenes ; Regulatory sequences ; Reptiles & amphibians ; RNA polymerase ; Tetraploidy ; Transposons ; Whole genome duplication ; Xenopus ; Xenopus laevis ; Xenopus laevis - genetics
É parte de: Genome Biology, 2017-10, Vol.18 (1), p.198-18, Article 198
Descrição: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers comprise transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos. The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and non-allelic homologous recombination and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole-genome duplication.
Editor: England: BioMed Central Ltd
Idioma: Inglês

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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Elurbe, Dei M ; Paranjpe, Sarita S ; Georgiou, Georgios ; van Kruijsbergen, Ila ; Bogdanovic, Ozren ; Gibeaux, Romain ; Heald, Rebecca ; Lister, Ryan ; Huynen, Martijn A ; van Heeringen, Simon J ; Veenstra, Gert Jan C

England: BioMed Central Ltd

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