Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters

Abstract

The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G₂/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Every cell contains a complete copy of the genome, which is comprised of DNA. To fit the genome into the cell nucleus, DNA strands are wound around spools made of proteins called histones. By packing DNA, histones also control access to DNA, which influences when genes can be turned on and off. The authors present two main findings. First, they demonstrate a new, simple method to determine how tightly genes are wrapped around histones. Second, they use the new method to determine what happens to DNA packaging at every gene through one cycle of cell growth and division. They find that as genes get turned on throughout the cell cycle, the packaging of DNA that controls those genes becomes loose, and as genes get turned off, it becomes tight again. However, some cell cycle–regulated genes do not fit this pattern, suggesting another means of regulation for these genes. Interestingly, cell cycle–related differences in packaging at single genes are smaller than differences in packaging that are always apparent between different groups of genes. This suggests that most differences in how DNA is packaged may be controlled by the sequence of DNA itself, with smaller contributions from other factors.