Silencing at the cryptic mating loci, HML
, in S. cerevisiae
requires silencers that recruit Orc1p, Rap1p, Abf1p and Sir1 to mediate silencing.21
The silencers recruit the Sir proteins, Sir2, Sir3 and Sir4, which bind nucleosomes to create a large domain of inaccessible and transcriptionally inert chromatin.
The establishment of silencing requires passage through the G2
/M phase of the cell cycle but does not require DNA replication.21
While the replication-independent S-phase event necessary to establish the silent state is not fully clear, the Sir proteins are unable to stably bind to chromatin during the G2
phase of the cell cycle and full silencing is only achieved in telophase concomitant with the degradation of cohesin subunits.21
While establishment of silencing requires passage through S-M, the silenced state once established is also disrupted in each cell cycle and must be faithfully re-established in every cell cycle following replication. The chromatin state after replication mimics euchromatin and therefore re-formation of the silenced chromatin is likely an active process. The proper deposition of nucleosomes during replication, removal of the acetyl marks by histones deacetylases and the even spacing of nucleosomes during chromatin maturation are all necessary for efficient inheritance of the silent state.22,23
Most importantly, the inheritance of the silenced state also requires the silencers. Deletion of the silencer in cells progressing through the cell cycle leads to de-repression of the silent domain within a single generation,24
indicating that an intact silencer is required for the efficient inheritance of the repressed chromatin structures following replication. The silencer appears to provide the genomic memory that promotes the reformation of the silent chromatin in the progeny.25
Furthermore, mutations in the silencer bound proteins indicate redundancies in the silencer. Mutations in any one silencer bound protein leads to an increase in the probability of loss of silencing26,27
presumably because the stability of the protein complex at the silencer is weakened and the probability of inheriting the repressed state is thus reduced. Thus silencers can be considered as elements that efficiently ensure epigenetic memory.
In addition to the silencers, it is likely that the Sir proteins are important for the efficient inheritance of the repressed state. SUM1-1
is a dominant mutation of the local repressor Sum1.21SUM1-1
is recruited to the silenced HMR
domain by the silencer bound proteins and represses genes even in the absence of the Sir proteins.21
However, unlike Sir mediated repression, the SUM1-1
mediated repressed state is not stably inherited28
suggesting that the silencers are not sufficient for inheritance and the Sir proteins either directly or indirectly also play a role.
Yeast silencers form distinct clusters at the nuclear membrane and the Sir proteins are highly concentrated at these clusters.29
Loss of the clusters in mutants of Sir4, Ku70/80 and Esc1 lead to a dispersal of Sir proteins and a concomitant decrease in silencing.30
Compartmentalization of silenced DNA to regions of the nucleus rich in specific repressors likely enhances the probability of epigenetic inheritance of the silent state and the same may well be true for gene activation.