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

Abstract

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 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.

Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos

“…Genome activation in Hydractinia is widespread across thousands of genes that were also expressed in the maternal contribution ( Fig 1B–1D ), similar to other animals [ 2 , 18 , 31 , 48 , 59 ]; as well as repetitive and transposon-associated elements, reinforcing a growing trend of the roles of transposons in shaping early embryonic gene expression across taxa by contributing regulatory sequences that can be co-opted to drive early gene activation [ 69 , 75 – 77 ]. However, it is the massive activation of histone gene transcription that underlies the major change to the blastula/gastrula transcriptome ( Fig 2 ).…”

“…Genome activation in Hydractinia is widespread across thousands of genes that were also expressed in the maternal contribution (Fig 1B -1D), similar to other animals [2,18,31,48,59]; as well as repetitive and transposon-associated elements, reinforcing a growing trend of the roles of transposons in shaping early embryonic gene expression across taxa by contributing…”

“…To detect subtler signals of embryonic genome activation, we quantified intronic sequencing read coverage. In other animals, a large proportion of de novo transcription at genome activation occurs for genes that already have a maternal RNA contribution, which can be difficult to dissect apart in RNA-seq data [ 2 , 18 , 31 , 48 , 57 – 59 ]. Previously, we demonstrated that RNA-seq reads mapping to intronic regions can detect de novo pre-mRNA production in maternal genes where increases in exonic read coverage are too modest to robustly quantify [ 18 , 59 ].…”

“…The factors guiding Hydractinia genome activation also remain to be discovered among the many maternally provided transcription factor mRNA ( Fig 4B ); however, notable in the maternal contribution was a predicted HMG-domain factor with similarity to vertebrate Sox2 and the POU-domain containing Polynem, previously associated with Hydractinia stem-cell induction [ 78 ]. Zebrafish Pou5f3 (Oct4 homolog) and Sox19b (Sox2 homolog) along with Nanog, and Xenopus Pou5f3 and Sox3 (Sox2 homolog) are also maternally provided and required for genome activation in their respective species [ 18 , 59 , 79 – 81 ]. POU-domain and HMG-domain factors are found in the ctenophore M .…”

“…The previously characterized POU-domain transcription factor Polynem, which is associated with embryonic and adult stem cells in Hydractinia echinata PLOS GENETICS [78], is also present in the maternal contribution (HyS0098.14), albeit at lower levels (Fig 4B and S10 Table). Sox2 and POU-homeobox Oct4 homeologs play major roles in mammalian pluripotent stem cell induction and genome activation in zebrafish and Xenopus, suggesting that similar factors may help guide Hydractinia genome activation [18,59,[79][80][81][82].…”