Chromatin structure and gene expression in Saccharomyces cerevisiae quiescence

Abstract

Eukaryotic DNA is packaged into chromatin, a nucleo-protein structure influencing various cellular functions. I was interested in understanding the connections between chromatin structure, gene expression, and cellular physiology in Saccharomyces cerevisiae during the extreme growth transition from exponential growth to quiescence. I thus measured genome-wide chromatin and proteomic changes during this transition.

At the nucleosome level protein-coding genes initially gained nucleosome occupancy on average with later gains occurring over promoter nucleosome depleted regions (NDRs). Individually, NDR occupancy and transcript level changes correlated negatively, especially for genes with large increases in NDR occupancy. Genes in the same functional class displayed similar changes potentially impacting expression via transcription factor binding site (TFBS) occlusion. Rpd3L-, ISWI-, and RSC-related TFBSs had decreased nucleosome occupancy with promoters containing RSC binding sites also having more TFBSs with lower nucleosome occupancy and increased transcript levels.

At the chromosome level interaction frequency between any two points within a chromosome arm decreased exponentially with increasing linear chromosomal distance for both growth states. Also, intra-arm interactions were more frequent than inter-arm or -chromosomal interactions, and intra-arm interactions formed domains of self-association with variable boundaries between states. These data accompanied by fluorescence microscopy revealed three changes to the spatial organization of chromosomes during quiescence. First, subtelomeric interactions and the number of telomeric foci increased reflecting increases in subtelomeric foci participation. Second, inter-centromeric interactions decreased suggesting spindle pole body reorganization. Third, chromosomes condensed as seen by global decreases in intra-chromosomal interactions and decreased average distance between two intra-chromosomal loci. Furthermore, conditional inactivation of condensin abolished this condensation in a large subpopulation of cells.

Finally, I measured proteomic changes upon the transition to quiescence induced by different nutrient starvations. Protein and transcript levels tended to concertedly change for nitrogen and phosphate but not glucose starvation. The number of post-starvation cell divisions appeared to govern this correlation. I identified nutrient-specific and -independent proteomic changes, each group enriched for different cellular functions. While many proteins changed in abundance these changes alone were not observed to significantly impact the functions of metabolic enzymes or genes required to survive quiescence when compared to the global proteome.