G1 length dictates heterochromatin landscape [ChIP-seq]

Stem cells have lower facultative heterochromatin as defined by trimethylation of histone H3 lysine 27 (H3K27me3) compared to differentiated cells. However, the mechanisms underlying these differential H3K27me3 levels remain elusive. Because H3K27me3 levels are diluted two-fold in every round of replication and then restored through the rest of the cell cycle, we reasoned that the cell cycle length could be a key regulator of total H3K27me3 levels. Here, we demonstrate that a fast cell cycle sets low levels of H3K27me3 in serum-grown murine embryonic stem cells (mESCs). Extending the G1 phase leads to an increase in global H3K27me3 in mESCs due to the formation of de novo Polycomb domains, and the length of the G1/S block correlates with the extent of gain in H3K27me3, arguing that levels of the modification depend on the time available between successive rounds of replication. Similarly, accelerating the G1 phase in HEK293 cells decreases H3K27me3 levels. Finally, we applied this principle in tumor cells harboring a dominant negative H3K27M allele that reduces H3K27me3 levels. In these cells, extending G1 increases H3K27me3 levels, pointing to an unexpected means to rescue the effect of oncohistones. Our results suggest cell cycle length as a universal mechanism to modulate heterochromatin formation and, thus, cellular identity. Overall design: Chromatin Immunoprecipitation and sequencing (ChIP-seq) for H3K27 trimethylation (H3K27me3) and H3K27 acetylation (H3K27ac) for mouse embryonic stem cells (mESCs) grown in serum/LIF or 2i media.