Summary Packaging of DNA into chromatin has a profound impact on gene expression. To understand how changes in chromatin influence transcription, we analyzed 165 mutants of chromatin machinery components in Saccharomyces cerevisiae. mRNA expression patterns change in 80% of mutants, always with specific effects, even for loss of widespread histone marks. The data is assembled into a network of chromatin interaction pathways. The network is function-based, has a branched, interconnected topology and lacks strict one-to-one relationships between complexes. Chromatin pathways are not separate entities for different gene sets, but share many components. The study evaluates which interactions are important for which genes and predicts new interactions, for example between Paf1C and Set3C, as well as a role for Mediator in subtelomeric silencing. The results indicate the presence of gene-dependent effects that go beyond context-dependent binding of chromatin factors and provide a framework for understanding how specificity is achieved through regulating chromatin.

To define the molecular regulators required for differential pattern of H3K79 methylation by Dot1, we performed a GPS screen and discovered that the components of the cell cycle-regulated SBF complex were required for normal levels of H3K79 di- but not trimethylation. Genome-wide mapping revealed that H3K79 di- and trimethylation to present a mutually exclusive pattern on chromatin with M/G1 cell-cycle-regulated genes significantly enriched for H3K79 dimethylation. Since H3K79 trimethylation requires prior monoubiquitination of H2B, we performed genome-wide profiling of H2BK123 monoubiquitination and showed that H2BK123 monoubiquitination is excluded from cell cycle regulated genes and sites containing H3K79me2 but not from H3K79me3 containing regions. A genome-wide screen for factors responsible for the establishment/removal of H3K79 dimethylation resulted in the identification of several genes including NRM1 and WHI3, which both impact the transcription by the SBF, and MBF complexes, further linking the regulation of H3K79’s methylation status to the cell cycle.

The expression of genes that reside near telomeres is attenuated through telomere position-effect variegation (TPEV). Using a URA3 reporter located at TEL-VIIL of S. cerevisiae, it was demonstrated that the disruptor of telomeric silencing-1 (Dot1) regulates TPEV by catalyzing the methylation of H3K79. URA3 was also used as a reporter to demonstrate that H3K79 methylation is required for HM silencing. Surprisingly, a genome-wide expression analysis of mutants defective in H3K79 methylation patterns indicated that only a few telomeric genes, such as the COS12 located at TEL-VIIL, are subject to H3K79 methylation-dependent natural silencing. Consistently, loss of Dot1 did not globally alter Sir2/3 occupancy in subtelomeric regions, but did lead to some telomere-specific changes. Furthermore, we demonstrated that H3K79 methylation by Dot1 does not play a role in the maintenance of natural HML silencing. Our results show that the commonly used URA3 reporter located at TEL-VIIL or at the mating loci may not report on natural PEV and that studies concerning the epigenetic mechanism of silencing in yeast should employ assays that report on the natural pattern of gene expression.