a, Distribution of representative conserved DNA motifs from four distribution classes. b, Distribution of all motifs plotted with Treeview46. Bin counts from all motifs in Fig. S12 were converted to fold deviations from the regional average (−/+ 1 kb), converted to a log₂ scale, and plotted. Red/black/green denotes above, near, or below average deviations, respectively.

a, Composite distribution of nucleosomes relative to ORF end points. Also shown is the distribution of transcript termination sites (polyA sites) in red. Nearby genes were either included (gray) or eliminated (black) from the analysis. b, Average correlation of all Drosophila gene terminal regions to AA/TT or CC/GG NPS patterns. The nucleosome profile from panel a is shown as a gray backdrop.

a, Composite distribution of WW and SS dinucleotides (as indicated) along the 147 bp axis of nucleosomal DNA (p-value = 0). The equivalent yeast profile1 is shown in light shading in the background. b, Average correlation of all Drosophila promoter regions to nucleosome positioning sequence (NPS) patterns, comparing an AA/TT and a CC/GG pattern. The distribution of H2A.Z nucleosomes from Fig. 1b is shown as a gray backdrop. The span of the +1 nucleosome is indicated by the horizontal bar.

a, Browser shot of an arbitrary locus (nbs-defl). Bar graph represents the number of “W” or “C” (top and bottom traces, respectively) strand reads mapped to each coordinate. b, Composite distribution of H2A.Z nucleosomes relative to the TSS. Nearby genes were either included (gray) or eliminated (black) from the analysis, and normalized accordingly. The equivalent Saccharomyces profile is shown in green1. c, Correlation of the number of H2A.Z nucleosomal sequencing reads (per gene) to mRNA levels in 8–12 hr embryos.

a, Genome-wide location of “Paused” Pol II relative to the TSS. ChIP-chip genomic profiling of Pol II was conducted on Drosophila embryos. The black filled plot shows the distribution of Pol II at 1,956 “Paused” Pol II genes (see Methods). The yellow trace shows the distribution of permanganate-reactive thymines (an indicator of pausing) in 50 genes that undergo pausing30. The distribution of Pol II at these 50 genes is similar to the bulk profile (Fig. S18a). b, H2A.Z nucleosomal distribution at 1,956 genes that contained “Paused” Pol II. The “Not paused” class represents those where Pol II is either absent or not paused. c, Distribution of Pol II-bound nucleosomes. Pol II ChIP was performed on bulk MNase-digested mono-nucleosomal DNA and hybridized to genome-wide tiling arrays. The three traces include distributions at 1,956 Pol II “Paused” genes, and control distributions either at 788 genes that have “No H2A.Z” within 1 kb of the TSS, or at 8,736 genes of the “Not paused” class.