This chapter presents the unique pattern of very early translational and transcriptomic clocks following genome activation in the zygote. This chapter shows that these clocks consist of numerous tissue-specific clocks coordinated in time, while functioning both acutely and over long periods of time. This chapter also shows the clocks of DNA modification and repair as a sum of inverse U-shaped curves of methylations during acute, very early embryonic phases, which peaks around mid-gestation. This chapter further shows data that contradicts accepted views on an existing negative correlation between the level of methylations and the level of receptor availability. This chapter integrates data showing that in healthy gestation an optimal range of methylation level is required at any given time and that this range narrows as gestation progresses and postnatally. This chapter also argues that DNA modifications regulate gene expression with the capacity of DNA insult repair, including the reactivity to maternal immune activation due to inflammation or exposure to pathogens, especially during early embryonic phases. It is shown that the development of neurobehavioral disorders is not obligatory due to such DNA insults. Finally, this chapter presents DNA modifications as tissue-specific and time-specific, while their peaking time parallels the time of emergence of very early human capacities at mid-gestation, upon reaching the borderline of viability. It is concluded that the timing of coordination between all tissue-specific transcriptomic clocks combining, upregulation of some genes with downregulation of others, is under the governance of clock genes that were found to exert an overarching architecture that affects the entire genome’s transcription in a time-sensitive manner.