Gradual and progressive loss of repressive marks from the four mouse Hox clusters during RA-induced differentiation. (A) ChIP-on-chip analysis shows a gradual loss of the H3K27me3 repressive mark and SUZ12 occupancy over each Hox cluster upon RA treatment. Although many of the Hox genes are expressed early in the time course, over a whole cluster, H3K27me3 is greatly reduced by 36 h of RA treatment. The gradual loss of repressive marks is observed from anterior to posterior genes in a Hox cluster over a time course correlating with colinearity. (B) Kinetics of reduction of SUZ12 occupancy over TSS of HoxA and HoxB genes in paralogy groups 1 and 9 during RA-induced differentiation of ES cells. Anterior Hox genes rapidly lose SUZ12 over their TSS, as illustrated by changes for Hoxa1 and Hoxb1 at 2 h of RA treatment; whereas posterior genes show little change over their TSS in this time frame. The differences in the kinetics of loss of SUZ12 between genes correlates with their respective time of activation. A 500-bp region around the TSS is shown, and a 50-bp region around TSS is marked by a light blue band. The y-axis shows relative levels of occupancy of SUZ12.
