Transcriptional regulatory logic of the diurnal cycle in the mouse liver
Fig 3
Genome-wide rhythms in DNase I signals are synchronous with RNA Polymerase II (Pol II) transcription and histone acetylation.
A. Number of DNase I hypersensitive sites (DHSs) with statistically significant cycling DNase I signals (left), H3K27ac signals (middle), or Pol II signals (right) at three different thresholds (p < 0.1, p < 0.05 and p < 0.01, harmonic regression), partitioned according to their genomic location: TSS (1 kb), proximal (1–10 kb from TSS), or distal (>10 kb from TSS). B. Comparison of log2 amplitudes for DHSs in each class (TSS, proximal, and distal) and in each signal (Pol II, H3K27ac, and DNase I). We selected 4,606 sites (FDR < 0.05, Fisher's combined test). Higher amplitudes were observed in distal and proximal regions compared to TSSs (p < 2.2*10−16, t test). In addition, Pol II loadings showed higher peak-to-trough ratios than the two other signals. C. Circular histograms representing the distributions of phases for each mark at DHSs selected as in B. D. Comparisons of peak times between DNase I, Pol II, and H3K27ac at DHSs (DHSs selected with p < 0.05, Fisher’s combined test), diagonals are indicated in gray. Values of circular correlations are indicated (p < 10−10, circular correlation). E. Relationships of peak times between DHSs in intergenic regions with their nearest TSS (pairs selected with FDR < 0.1, Fisher’s combined test). We found 1,611 and 630 significant pairs for H3K27ac and Pol II signals, respectively.