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. Overall design: CUT&Tag of mESCs cultures in Serum/LIF, EMM, or EMM plus NAM. Sirt1 mutants were cultured in Serum/LIF and EMM