FIGURE 2: Expression dynamics of major gene clusters and the DNA occupancy dynamics at their average gene promoters during a respiratory cycle.

Messenger RNA abundances from the consensus clusters (Clusters A, AB, B, C and D; [19]) from a time-series microarray dataset [26] (48 samples; 4 min sampling, period 50 min) were summed for each cluster (A), ∑[mRNA]. Transcripts that belong to the anabolic supercluster (A, AB and B; produced during the oxidative phase) and those that belong to the catabolic supercluster (C and D; produced during the reductive phase) have a solid red and blue fill, respectively. The median DNA occupancy profiles of the aligned nucleosome dyads for the consensus clusters during a respiratory cycle ((B), DNA occ) were calculated as in Figure 1B. The DNA occupancy dynamics ((C), ΔDNA occ) were normalized by subtracting the log-ratio temporal average (red and blue side bar) from the median DNA occupancy for each expression cluster (see Fig. 1A). Dotted lines represent the residual dissolved oxygen (DO), scaled to the y-axis range of the panel. The transcript and nucleosome datasets were aligned using the minimum and maximum first derivative of the DO (Fig. S4A). The minimum first derivative of the DO data represents 0°/360°. The differential expression clusters B.C and B.D were merged into an expanded cluster B, as these were co-expressed during the short period oscillation. These clusters and lower signal-to-noise ratio clusters are shown in Figure S3.

19. Machné R and Murray DB (2012). The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin. PLoS One 7(6): e37906. http://dx.doi.org/10.1371/journal.pone.0037906
26. Li CM and Klevecz RR (2006). A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc Natl Acad Sci U S A 103(44): 16254–16259. http://dx.doi.org/10.1073/pnas.0604860103