Fig. 5
The transcriptional and temporal coordination of oscillating modified cytosines in the 9-mo mouse liver and lung. a, b Mean gene-body modification densities of epigenetically variable cytosines in a the liver and b the lung were cross-correlated with corresponding circadian mRNA profiles after each iteration of a forward 1 h phase shift in the mRNA profiles. Bars represent the observed mean cross-correlation between mRNAs and modification densities for a given phase shift (red bars indicate Bonferroni corrected permuted p < 0.05). The positive faded bars are mirror images of the negative bars (by nature of correlating phase shifted waves, a wave shifted by half a period anti-correlates with itself). Fine gray curves in the background depict cross-correlations of 100 randomly selected (out of 10,000) permutations where both ZT labels and mRNA-gene modification density pairs were shuffled. c, d Representative E-box motifs enriched within 100 bp in either direction of osc-modCs in c the mouse liver and d the lung. e, f Harmonic regression fits on the average modification density of osc-modCs with wake and sleep acrophases in e the mouse liver and f the lung, as a function of ZT. Shading around the regression lines represents the 95% confidence band. ZT, Zeitgeber time; modC, cytosine modification
