Mouse embryonic stem cells (mESCs) cultured in the presence of LIF occupy a ground state with highly active pluripotency-associated transcriptional and epigenetic circuitry. However, ground state pluripotency in some inbred strain backgrounds is unstable in the absence of ERK1/2 and GSK3 inhibition. Using an unbiased genetic approach, we dissect the basis of this divergent response to extracellular cues by profiling gene expression and chromatin accessibility in 170 genetically heterogeneous mESCs. We map thousands of loci affecting chromatin accessibility and/or transcript abundance, including 10 QTL hotspots where genetic variation at a single locus coordinates the regulation of genes throughout the genome. For one hotspot, we identify a single enhancer variant ∼10 kb upstream of Lifr associated with chromatin accessibility and mediating a cascade of molecular events affecting pluripotency. We validate causation through reciprocal allele swaps, demonstrating the functional consequences of noncoding variation in gene regulatory networks that stabilize pluripotent states in vitro.

在 LIF 存在下培养的小鼠胚胎干细胞 (mESCs) 占据具有高度活跃的多能性相关转录和表观遗传电路的基态。然而，在没有 ERK1/2 和 GSK3 抑制的情况下，一些近交系背景中的基态多能性是不稳定的。使用无偏见的遗传方法，我们通过分析 170 个遗传异质性 mESC 中的基因表达和染色质可及性来剖析这种对细胞外线索的不同反应的基础。我们绘制了数千个影响染色质可及性和/或转录本丰度的基因座，包括 10 个 QTL 热点，其中单个基因座的遗传变异协调整个基因组的基因调控。对于一个热点，我们确定了Lifr上游∼10 kb 的单个增强子变体与染色质可及性相关并介导影响多能性的一系列分子事件。我们通过相互等位基因交换来验证因果关系，证明了在体外稳定多能状态的基因调控网络中非编码变异的功能后果。