Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [ATAC-seq]

Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs. Mapping changes in chromatin accessibility using ATAC-seq during in vitro differentiation of mouse embryonic stem cells into primitive endoderm. Please note that the records have been updated with additional processed data *bfilt.bed files on June 16th, 2022.

由共同祖细胞分化为多种不同细胞类型，需要转录因子（transcription factors, TFs）在抑制其他备选细胞命运的同时，促进谱系限制性的转录程序。在小鼠囊胚中，内细胞团（inner cell mass, ICM）的细胞共表达NANOG与GATA6这两种转录因子，二者分别驱动这些祖细胞分化为上胚层（epiblast, Epi）或原始内胚层（primitive endoderm, PrE）。本研究借助体外分化实验，阐明了GATA6如何快速诱导原始内胚层命运，并同时抑制上胚层谱系的分子机制。

GATA6作为先驱转录因子（pioneer TF），在调控原始内胚层基因的调控元件处诱导核小体重定位，使该区域可结合活性组蛋白修饰，进而重塑染色质相互作用网络，最终实现转录激活。GATA6同时结合绝大多数上胚层基因的调控元件，随后驱逐上胚层特异性转录因子NANOG与SOX2，导致活性组蛋白修饰丢失、染色质可及性降低，最终实现转录抑制。

令人意外的是，被驱逐的NANOG与SOX2会短暂结合GATA6所占据的原始内胚层调控元件。本研究证实，GATA6可结合并调控与上胚层转录因子相同的调控元件，这一现象在小鼠囊胚中也得到了验证。我们提出，原始内胚层与上胚层特异性转录因子能够广泛结合并调控同一基因网络的特性，促成了内细胞团的细胞可塑性，并通过协同激活与抑制不同的转录程序，实现快速的细胞谱系特化。

本研究通过ATAC-seq（转座酶可及性测序），绘制了小鼠胚胎干细胞向原始内胚层体外分化过程中染色质可及性的动态变化图谱。请注意，本数据集的记录已于2022年6月16日更新，新增了经处理的*bfilt.bed格式文件。