FIGURE 3: Defining the reset point of the respiratory oscillation.

The temporal profile of the DNA occupancy (DNA occ) at the center of the nucleosome region for the anabolic and catabolic superclusters (A) were calculated as in Figure 1B. Histone H3 (B) and H3K9ac ((C), log-ratio values with respect to H3) ChIP time-series (14 samples; 4 min sampling; period 53 min) were amplified by qPCR at TSS regions of 4 representative anabolic (red hues) and catabolic (blue hues) genes. Total mRNA abundances for each supercluster ((D), ∑[mRNA]) were used to calculate mRNA abundance rate of change ((E); ∑[mRNA]’; change in mRNA abundance every 15°). The same samples for B and C were used for RNA PolII ChIP-qPCR at genome body regions of 4 representative anabolic (red hues) and catabolic (blue hues) genes (F). The PolII signals were normalized with respect to a subtelomeric region on chromosome VI. ATP, ADP and AMP concentration time-series data ((G), 36 samples, 6 min sampling, period 78 min, Fig. S4B) measured by capillary electrophoresis mass spectrometry [30] were used to calculate inferred ISWI remodeling rates (H). An average cycle was constructed by a cubic spline fitting for each time-series spanning several cycles (A, D, E, G, H). Error bars in B, C, F represent standard error of mean of qPCR triplicates. Dotted lines represent the residual dissolved oxygen (DO), scaled to the y-axis range of each panel, and datasets were aligned using the minimum and maximum first derivative of DO concentration (Fig. S4A). The minimum first derivative of the DO data represents 0°/360°. The anabolic supercluster was defined as clusters A, AB, B, B.C, B.D and ab.n and the catabolic supercluster was defined as clusters C, D, cd.n and cd.ab.

30. Sasidharan K, Soga T, Tomita M, and Murray DB (2012). A yeast metabolite extraction protocol optimised for time-series analyses. PLoS One 7(8): e44283. http://dx.doi.org/10.1371/journal.pone.0044283