Changes in the genome-wide localization pattern of Sir3 in Saccharomyces cerevisiae during different growth stages

In budding yeast, the Sir2, Sir3 and Sir4 proteins form SIR complexes, required for the assembly of silent heterochromatin domains, and which mediate transcription silencing at the telomeres as well as at silent mating type loci. In this study, under fluorescence microscopy, we found most Sir3-GFP expressions in the logarithmic phase cells appeared as multiple punctations as expected. However, some differences in the distribution of fluorescent signals were detected in the diauxic~early stationary phase cells. To clarify these, we then used ChIP on chip assays to investigate the genome-wide localization of Sir3. In general, Sir3 binds to all 32 telomere proximal regions, the silent mating type loci and also binds to the rDNA region. However, the genome-wide localization patterns of Sir3 are different between these two distinct growth phases. We also confirmed that Sir3 binds to a recently identified secondary binding site, PAU genes, and further identified 349 Sir3-associated cluster regions. These results provide additional support in roles for Sir3 in the modulation of gene expression during physical conditions such as diauxic~early stationary phase growing. Moreover, they imply that Sir3 may be not only involved in the formation of conventional silent heterochromatin, but also able to associate with some other chromatin regions involved in epigenetic regulation.