Figure 1.

DHSs exhibit programmed developmental changes (a,b). Developmental profiling at ftz and brk loci. The density of mapped DNaseI cleavages (150-bp sliding window, step 20 bp) is shown for stages 5 (green), 9 (orange), 10 (red), 11 (blue) and 14 (purple) across a 50-kb region of the D. melanogaster genome that includes the (a) ftz and (b) brk genes. Locations of known cis-regulatory modules (CRMs) are indicated with red bars and underlying shaded regions. CRMs shown are all known to be active at stage 5 and inactive at later stages except the one indicated with an asterisk, which is a neuronal CRM active after stage 5. Temporally dynamic patterning of chromatin accessibility at DHSs is evident in up- and down-regulation of accessibility during embryo development. (c) High reproducibility of DNaseI sensitivity profiles. The pairwise Pearson correlations between DNase I cleavage density datasets from different stages (or between replicates of the same stage, along the diagonal) are indicated in a spectrum from red (extremely high correlation) to white (moderate correlation). The largest differences are observed between stage 14 and earlier stages. (d) Developmental propogation of DHSs. Stage 9 DHSs were divided into two groups, those observed at stage 5 and those that arise during the transition from stages 5 to 9. Likewise for stages 10, 11, and 14 the percentages of DHSs are depicted according to stage of temporal origin: stage 5 (green), 9 (orange), 10 (red), 11 (blue) and 14 (purple). The majority of sites (approximately 55%) observed at stage 5 are carried forward through stage 14.