Abstract
The establishment of silent chromatin, a heterochromatin-like structure at HML and HMR in Saccharomyces cerevisiae, depends on progression through S phase of the cell cycle, but the molecular nature of this requirement has remained elusive despite intensive study. Using high-resolution chromatin immunoprecipitation and single-molecule RNA analysis, we found that silencing establishment proceeded via gradual repression of transcription in individual cells over several cell cycles, and that the cell-cycle-regulated step was downstream of Sir protein recruitment. In contrast to prior results, HML and HMR had identical cell-cycle requirements for silencing establishment, with no apparent contribution from a tRNA gene adjacent to HMR. We identified the cause of the S-phase requirement for silencing establishment: removal of transcription-favoring histone modifications deposited by Dot1, Sas2, and Rtt109. These results revealed that silencing establishment was absolutely dependent on the cell-cycle-regulated interplay between euchromatic and heterochromatic histone modifications.
Highlights
Inheritance of gene expression state often accompanies the inheritance of genetic content during cell division
During development, cell division is coupled to the rewiring of gene expression patterns that lead to the generation of new cell types
The silent chromatin controlling mating-type identity in Saccharomyces cerevisiae offers a tractable context for exploring how cell-cycle-regulated chromatin dynamics lead to the establishment of new expression states
Summary
Inheritance of gene expression state often accompanies the inheritance of genetic content during cell division. During development, cell division is coupled to the rewiring of gene expression patterns that lead to the generation of new cell types. An understanding of chromatin and epigenetics requires an understanding of the mechanisms by which cells can both faithfully transmit chromatin state through cell division, as well as subvert that inheritance in order to establish new cell types. The silent chromatin controlling mating-type identity in Saccharomyces cerevisiae offers a tractable context for exploring how cell-cycle-regulated chromatin dynamics lead to the establishment of new expression states. HML and HMR are flanked by DNA sequences termed silencers, which recruit the DNA-binding proteins Rap, Abf, and ORC. These in turn recruit the Sir proteins via protein-protein interactions. Sir protein recruitment to silencers is followed by the spread of Sir proteins across the multi-kilobase loci by iterative cycles of deacetylation of the tails of histones H3 and H4 by Sir and binding of Sir and Sir to those deacetylated histone tails(Hecht et al, 1995; Hoppe et al, 2002; Rusché et al, 2002)
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