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

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. ATAC-seq was performed on animal caps from Stage 8-9 embryos.

受精后，母源因子启动了卵子向多能性状态的转变，其核心机制在很大程度上通过激活胚胎基因组的新生转录实现。不同动物类群中存在多样化的调控机制以协调这一转变过程，这表明广泛的进化创新塑造了发育的早期阶段。本研究发现，哺乳动物重编程因子OCT4与SOX2的同源蛋白对异源四倍体非洲爪蟾（Xenopus laevis）的两个亚基因组进行差异化调控，最终导致早期胚胎内数百个部分同源基因对（homeologous gene pairs）出现不对称激活。通过染色质可及性谱分析以及针对修饰组蛋白和转录因子结合的CUT&RUN实验，本研究揭示了两个亚基因组之间增强子结构的广泛差异，这类差异大概率产生于约1700万年前非洲爪蟾二倍体祖先的杂交事件之后。然而，与二倍体热带爪蟾（X. tropicalis）的对比显示，当整合差异化的部分同源基因贡献时，胚胎基因的表达水平整体保持保守，这意味着在杂交引发的基因组不稳定背景下，多能性转录程序中存在维持剂量的强烈选择压力。本研究的ATAC-seq实验取材于第8-9期胚胎的动物帽组织。