Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions

Heterochromatin domains are stably repressed chromatin structures composed of a core assembly of silencing proteins that condense adjacent nucleosomes. The minimal heterochromatin structure can serve as a platform for recruitment of complementary regulatory factors. We find that a reconstituted budding yeast heterochromatin domain can act as a platform to recruit multiple factors that play a role in regulating heterochromatin function. We uncover the direct interaction between the SIR heterochromatin complex and a chromosomal boundary protein that restricts the spread of heterochromatin. We find that the SIR complex relieves a mechanism of auto-inhibition within the boundary protein Yta7, allowing the Yta7 bromodomain to engage chromatin. Our results suggest that budding yeast shares with other eukaryotes the ability to establish complex heterochromatin domains that coordinate multiple mechanisms of silencing regulation through physical interactions.