Cell cycle analysis of histone marks and 4C in human Fucci ESCs

Using the Fucci cell cycle indicator system in hESCs, we evaluated the patterns of bivalent histone marks and enhancer histone marks during the cell cycle by ChIP-seq. We further evaluated how the chromatin architecture changed during the cell cycle. We found that bivalent domains are cell cycle regulated, and H3K4me3 specifically peaks during the late G1 stage of the cell cycle. H3K27me3, however, is largely unchanged during the cell cycle. Cell cycle-regulated bivalent domains interact with enhancers and form cell cycle regulated chromatin interactions. Overall design: FACS-isolated cell cycle fractions (DN, early G1; KO2, late G1; AzL, S-phase; and AzH, G2/M) from Fucci hESCs were subject to ChIP-seq for H3K4me3, H3K27me3, H3K27ac and H3K4me1, and used for sequencing along with input controls for each of the 4 cell cycle fractions (20 samples total), using Illumina platform, or 4C-seq for each cell cycle fraction using viewpoints neighboring the GATA6 or SOX17 promoters.