Altering metabolism programs cell identity via NAD+-dependent deacetylation [CUT&Tag]

Cells change their metabolic profiles in response to underlying gene regulatory networks, but how can alterations in metabolism encode specific transcriptional instructions? Here, we show that forcing a metabolic change in embryonic stem cells (ESCs) promotes a developmental identity that better approximates the inner cell mass (ICM) of the early mammalian blastocyst in cultures we refer to as enhanced metabolic ESCs (EMESCs). The creation of EMESCs depends on inhibition of glycolysis and stimulation of oxidative phosphorylation (OXPHOS), that in turns activates NAD+-dependent deacetylases of the Sirtuin family, resulting in the deacetylation of histones and key transcription factors to focus enhancer activity while reducing transcriptional noise, that result in a robust enhanced ESC phenotype. This exploitation of a NAD+/NADH coenzyme coupled to OXPHOS as a means of programming lineage specific transcription suggests new paradigms for how cells respond to alterations in their environment, and implies cellular rejuvenation exploits enzymatic activities to for simultaneous activation of a discrete enhancer set alongside silencing genome-wide transcriptional noise. CUT&Tag of mESCs cultures in Serum/LIF, EMM, or EMM plus NAM. Sirt1 mutants were cultured in Serum/LIF and EMM

细胞会响应内在基因调控网络改变自身代谢谱，但代谢改变如何编码特定的转录指令？本研究证实，对胚胎干细胞（ESCs）施加代谢扰动，可使其发育特征更贴近早期哺乳动物囊胚的内细胞团（ICM），我们将该培养体系下的细胞命名为增强代谢型胚胎干细胞（EMESCs）。EMESCs的构建依赖于糖酵解抑制与氧化磷酸化（OXPHOS）激活，该过程会激活沉默信息调节因子（Sirtuin）家族的烟酰胺腺嘌呤二核苷酸（NAD+）依赖型脱乙酰酶，进而引发组蛋白与关键转录因子的脱乙酰化，聚焦增强子活性并降低转录噪声，最终形成稳定的增强型ESC表型。这种将NAD+/NADH辅酶与氧化磷酸化耦合，用于调控谱系特异性转录的策略，为解析细胞如何响应环境改变提供了全新范式，同时提示细胞复壮可通过酶促活性，同时激活离散的增强子集合并沉默全基因组范围的转录噪声。本研究对血清/白血病抑制因子（Serum/LIF）、EMM或添加烟酰胺（NAM）的EMM培养体系中的小鼠胚胎干细胞（mESCs）开展了CUT&Tag分析；同时在Serum/LIF与EMM培养体系中培养了Sirt1突变体。