Figure 1. Crystal structures of the yeast nucleosome in complex with the BAH domain of Sir3. Sir3 binds to the tail of histone H4 via contacts with K16 and H18, and induces contacts between R17 and R19 with nucleosomal DNA. The resulting argenine “clamp” is required for silencing. From Wang et al., 2013, PNAS.
Figure 2. Association of the Sir3 silencing protein with mono- and di-nucleosomes. (A) Biolayer Interferometry Assay (BLI) for assessing the binding of Sir3 to reconstituted nucleosomes. The nucleosome is immobilized on the sensor using a biotin linker. Association of Sir3 results in a change in refractive indenx of reflected light which is measured in real time. (B) binding curves for the association of the BAH domain of Sir3 (Sir3BAH) and full-length Sir3 with mono- and di-nucleosomes (MonoN and DiN, respectively), showing greatly increased affinity of full-length Sir3 for DiN. From Behrouzi, Lu, et al., 2016, eLife.
Figure 3. Model for association of the SIR complex with chromatin based on the nucleosome-binding properties of the Sir3 and the SIR complex. From Behrouzi, Lu, et al., 2016, eLife.