Interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression

A two-colour cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. We describe a fluorescent reporter system that exploits the functional genomic tools available in budding yeast to systematically assess consequences of genetic perturbations on gene expression. We used our Reporter-Synthetic Genetic Array (R-SGA) method to screen for regulators of core histone gene expression. We discovered that the histone chaperone Rtt106 functions in a pathway with two other chaperones, Asf1 and the HIR complex, to create a repressive chromatin structure at core histone promoters. We found that activation of histone (HTA1) gene expression involves both relief of Rtt106-mediated repression by the activity of the histone acetyltransferase Rtt109 and restriction of Rtt106 to the promoter region by the bromodomain-containing protein Yta7. We propose that the maintenance of Asf1/HIR/Rtt106-mediated repressive chromatin domains is the primary mechanism of cell cycle regulation of histone promoters. Our data suggest that this pathway may represent a chromatin regulatory mechanism that is broadly used across the genome. The supplemental CEL files contain the raw hybridization signals from genome-wide nucleosome occupancy experiments in rtt106, hir1 and wild type strains. The .BAR files contain the normalized data for each mutant and wild-type compared to the total genomic DNA signal to identify nucleosome positions, as well as the data for each mutant normalized to the wild-type profile to visualize changes in occupancy compared to wild type conditions.