Genome-wide H2A.X deposition in mouse ESC orchestrated by environmental cue-induced demethylation

Epigenetic landscape in pluripotent stem cells undergoes dynamically changes in response to environmental cues. For example, recent studies suggest that long-term culture of mouse embryonic stem cells (ESCs) in the presence of Mek1/2 and Gsk3ß inhibitors (2i culture) leads to the irreversible loss of 5mC and its oxidative derivatives (5hmC, 5fC, and 5caC) as well as genomic redistribution of the histone variant H2A.X, which underlie the impaired developmental potential. However, it remains unclear whether such epigenetic changes are mechanistically connected or merely coincidental. In this study, we demonstrate that the accumulation of oxidative derivatives of 5mC, i.e. 5fC/5caC, serve as potent upstream signals for recruiting H2A.X in ESCs. Furthermore, our data suggest that global H2A.X redistribution in 2i cultured ESCs is due to the loss of 5fc/5caC. We show that the 2i condition also diminishes a recently discovered DNA modification, N6-mA. Moreover, we find that alternative culture conditions, which maintain normal developmental potential, can preserve 5mC and its derivatives, N6-mA and H2A.X deposition in ESCs. Taken together, our results revealed that rare DNA epigenetic modifications and histone variant serve as genome sensors for environmental cues in ESCs and early development. Overall design: H2A.X ChIP-seq in mouse ESCs