ArticleGenome biology2017
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 43 citations in OpenAlex.
- Liver-specific enhancers evolved from independent episodes of MITE domestication in Xenopus tropicalis.Mobile DNA · 2025Article
- The two sub-genomes of the allotetraploid frog Xenopus laevis are evolving under similar selective pressure in extant populations.BMC genomics · 2025Article
- Transposable element dynamics in Xenopus laevis embryogenesis: a tale of two coexisting subgenomes.Mobile DNA · 2025Article
- Evolution and function of galectins inBBA advances · 2025Article
- Rapid Sex Chromosome Turnover in African Clawed Frogs (Xenopus) and the Origins of New Sex Chromosomes.Molecular biology and evolution · 2024Article
- Correlation Between Subgenome-biased DNA Loss and DNA Transposon Activation Following Hybridization in the Allotetraploid Xenopus Frogs.Genome biology and evolution · 2024Article
- Article
- Temporal Transcriptomic Profiling of the DevelopingbioRxiv : the preprint server for biology · 2024Article
- Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus.BMC biology · 2023Article
- Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species.Nucleic acids research · 2023Article
- Article
- Modification of maternally defined H3K4me3 regulates the inviability of interspecificScience advances · 2023Article
- Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa.G3 (Bethesda, Md.) · 2023Article
- Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.Nature communications · 2023Article
- Ventx Family and Its Functional Similarities with Nanog: Involvement in Embryonic Development and Cancer Progression.International journal of molecular sciences · 2022Review
- Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System.BMC genomics · 2022Article
- Pharmacological modulation of the cAMP signaling of two isoforms of melanocortin-3 receptor by melanocortin receptor accessory proteins in the tetrapod Xenopus laevis.Endocrine connections · 2021Article
- The DNA-to-cytoplasm ratio broadly activates zygotic gene expression in Xenopus.Current biology : CB · 2021Article
- Conserved role of the urotensin II receptor 4 signalling pathway to control body straightness in a tetrapod.Open biology · 2021Article
- Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon.Genome biology and evolution · 2021Article
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Authors and funding
11 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundGenome 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.
resultsThe 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.
conclusionsThe 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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