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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

ABSTRACT: Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

OTHER RELATED OMICS DATASETS IN: GSE106157

PROVIDER: PRJNA357404 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5110210.fastq.gz	Fastqsanger.gz
	SRR5110220_1.fastq.gz	Fastqsanger.gz
	SRR5110220_2.fastq.gz	Fastqsanger.gz
	SRR5110211.fastq.gz	Fastqsanger.gz
	SRR5110221_1.fastq.gz	Fastqsanger.gz

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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Project description:Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates.The most recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. Here we generated epigenetic profiles and determined gene expression in X.laevis embryos to study the consequences of this duplication at the level of the genome, the epigenome and gene expression.

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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Project description: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.

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Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes

Project description:RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species. mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed.

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