PT - JOURNAL ARTICLE AU - Dei M. Elurbe AU - Sarita S. Paranjpe AU - Georgios Georgiou AU - Ila van Kruijsbergen AU - Ozren Bogdanovic AU - Romain Gibeaux AU - Rebecca Heald AU - Ryan Lister AU - Martijn A. Huynen AU - Simon J. van Heeringen AU - Gert Jan C. Veenstra TI - Regulatory remodeling in the allo-tetraploid frog <em>Xenopus laevis</em> AID - 10.1101/120212 DP - 2017 Jan 01 TA - bioRxiv PG - 120212 4099 - http://biorxiv.org/content/early/2017/03/24/120212.short 4100 - http://biorxiv.org/content/early/2017/03/24/120212.full AB - Background 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, resulting from the hybridization of two closely related species about 17 million years ago [1]. However, little is known about the consequences of this duplication at the level of the genome, the epigenome and gene expression.Results Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes ever since the genome duplication and 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 (NAHR) has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300 (Ep300)-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers are comprised of 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.Conclusions The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and NAHR, and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole genome duplication.