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Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE207027 | GEO | 2022/09/13

REPOSITORIES: GEO

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Hybridization led to a rewired pluripotency network in the allotetraploid <i>Xenopus laevis</i>.

Project description:After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency to give rise to embryonic stem cells, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that pervasive regulatory remodeling has shaped the earliest stages of development. Here, we show that maternal homologs of mammalian pluripotency reprogramming factors OCT4 and SOX2 divergently activate the two subgenomes of Xenopus laevis, an allotetraploid that arose from hybridization of two diploid species ~18 million years ago. Although most genes have been retained as two homeologous copies, we find that a majority of them undergo asymmetric activation in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in predicted enhancer architecture between the subgenomes, which likely arose through genomic disruptions as a consequence of allotetraploidy. However, comparison with diploid X. tropicalis and zebrafish shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the core vertebrate pluripotency transcriptional program, amid genomic instability following hybridization.

| S-EPMC10569791 | biostudies-literature

Hybridization led to a rewired pluripotency network in Xenopus laevis [ATAC-seq]

Project description:After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that widespread evolutionary innovation has shaped the earliest stages of development. Here, we show that homologs of mammalian reprogramming factors OCT4 and SOX2 divergently regulate the two subgenomes of the allotetraploid Xenopus laevis, resulting in asymmetric activation of hundreds of homeologous gene pairs in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in enhancer architecture between the subgenomes, which likely arose after hybridization of X. laevis's diploid progenitors ~17 million years ago. However, comparison with diploid X. tropicalis shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the pluripotency transcriptional program, amidst genomic instability following hybridization.

2022-09-14 | GSE207024 | GEO

Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq]

2022-09-14 | GSE207026 | GEO

Hybridization led to a rewired pluripotency network in Xenopus laevis [CUT&RUN]

2022-09-14 | GSE207025 | GEO

Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

Project description:Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

| PRJNA853331 | ENA

Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq]

Project description:Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq]

| PRJNA853335 | ENA

Hybridization led to a rewired pluripotency network in Xenopus laevis [CUT&RUN]