Everything oscillates, especially in biology. When yeast cells are grown to high cell density in liquid culture, they tend to synchronize their metabolic activity exposing an otherwise hidden layer of cellular dynamics. Known as respiratory oscillations, due to varying oxygen concentration as our major read-out, these dynamics are in line with an emerging picture of a fundamentally periodic nature of cell growth, where multiple distinct pulses of growth (translation!) can occur independent of and upstream of the cell division cycle. After these growth pulses, we observe a phase of little metabolic activity. The ATP/ADP ratio, pH and metabolic heat production reach minima, i.e., cells literally cool down. Both promoter and gene body chromatin undergo genome-wide reset points. K\(^+\) concentration peaks. The remaining low-level ATP synthesis is mostly used for build-up of storage material (glycogen or lipid droplets).
Here, I speculate that this phase may not only be analogous but homologous to human sleep. Newly synthesized proteins and other macromolecular structures can self-assemble, the cytoplasm becomes granular. In the nucleus, DNA torsional stress from the previous phase of strong transcription can be resolved, and loci of increased stress can be marked and adapted. Thus, this phase is akin not only to sleep but even involves dreaming where the activities during the previous growth pulses are echoed in DNA structure, and integrated into a new chromatin state, i.e., epigenetic memory can be established. Transposons (mobile regulatory elements) may target such stressed loci and thereby buffer transcription-induced stress during subsequent growth pulses, and provide a substrate for the rewiring of transcriptional regulation.
Learn all more about yeast and the YRO in my PhD thesis (2017). Some of the analyses
presented here are published in a
series (v1-v5) of desk-rejected bioRxiv revisions (Machné et al.
2021). More recent material can be found in the YRO
lecture series.
idk, ask them ;)
© Rainer Machné (2025)