Fig. 3

Signal intensity profiles of H3K4me3, H3K27me3 and RNAPolII enrichments at the Hoxa cluster; shown is the temporal signal evolution from consecutive ChIP-seq experiments during retinoic acid-induced differentiation of F9 cells. Most of the genes in Hoxa cluster have been shown to follow collinear gene activation pattern during differentiation with gradual increase of active marks and decrease of repressive marks. However, such pattern was not apparent from the raw RCI profiles. Data normalization resulted in the expected gradual spatio-temporal decrease of the H3K27me3 profile and concomitant increase of H3K4me3 & RNA PolII intensity profiles. The bottom panels reveal ChIP-qPCR analyses for H3K27me3, thus validating the normalization. Specifically Hoxa1, Hoxa3 and Hoxa4 genes - but not the Hoxa10 gene –follows a collinear gene activation pattern, as observed in both the normalized data and the qPCR results