The budding yeast heterochromatic protein Sir3 is a global modulator of gene expression

AbstractThe SIR complex (Silent Information Regulator) is the building block of heterochromatic structures that silence underlying genes. It is well established that the silenced state is epigenetically inherited but it is not known how the SIR complex survives perturbations caused by DNA replication nor how it is maintained when cells are exposed to environmental challenges such as nutrient deprivation. The biological function of heterochromatin located in subtelomeric regions is also unclear since heterochromatin coverage appears to be limited to a few kbps near chromosome ends and the expression of subtelomeric genes is only marginally affected in the absence of the SIR complex. We use a three pronged approach to address these questions. First, nanopore-MetID, an in vivo foot printing technique similar to DamID that uses nanopore sequencing technology, identified hundreds of new transient contacts between Sir3 and euchromatic genes that are not detectable by ChIP-seq and revealed a high and a previously undocumented low-density mode of Sir3 binding to subtelomeric regions. Second, our measurements of genome-wide Sir3 exchange rates after exit from starvation show that heterochromatin is a highly dynamic structure in optimal growth conditions. Third, “spike-in” RNA-seq time course experiments in the same conditions reveal that Sir3 modulates global mRNA levels in correlation with fluctuations in nutrient availability. We now propose that subtelomeric regions serve as Sir3 hubs from which Sir3 diffuses down the chromosome arm and transiently contacts euchromatic genes in its path. We hypothesize that contacts between Sir3 and actively transcribed genes facilitate the removal of stalled transcription complexes and allow for optimal genome-wide transcription.