| Topic | Key finding (with numbers where available) | System/assay | Source (author year, venue) | URL |
|---|---|---|---|---|
| Target identity and core function | SIR3/P06701 in *S. cerevisiae* is the structural, nucleosome-binding silencing subunit of the Sir2/3/4 complex; it contains an N-terminal BAH domain and a C-terminal AAA-like region implicated in chromatin interactions and oligomerization (pqac-00000005, pqac-00000007) | Genetics/biochemistry/structural synthesis | Currie et al. 2024, *Chromatin Readers in Health and Disease*; Buchberger et al. 2008, *MCB* | https://doi.org/10.1016/b978-0-12-823376-4.00006-9 ; https://doi.org/10.1128/mcb.01210-08 |
| BAH–nucleosome structure | Sir3 BAH was solved bound to the nucleosome at 3.0 Å; two Sir3 BAH domains bind one nucleosome (one per face) and make extensive contacts with all four core histones (pqac-00000000, pqac-00000003) | X-ray crystallography of Sir3 BAH–nucleosome complex | Armache et al. 2011, *Science* | https://doi.org/10.1126/science.1210915 |
| Histone-mark sensitivity | The Sir3 BAH domain binds the H4 tail and contacts the H3/H4 LRS region; silencing-relevant residues H4K16 and H3K79 are directly implicated, and H4K16 acetylation/H3K79 methylation impair Sir3 association with nucleosomes (pqac-00000000, pqac-00000001, pqac-00000003) | Structural biology plus biochemical/genetic synthesis | Armache et al. 2011, *Science*; Currie et al. 2024, book chapter | https://doi.org/10.1126/science.1210915 ; https://doi.org/10.1016/b978-0-12-823376-4.00006-9 |
| Canonical read–write logic of spreading | Sir2 deacetylates H4K16; Sir3 recognizes deacetylated H4K16-containing nucleosomes; Sir3 dimers, linked through Sir4 dimers, support cooperative binding to paired nucleosomes and cis-spreading of silent chromatin from silencers (pqac-00000012) | Mechanistic synthesis/engineered silent chromatin design | Yuan & Moazed 2024, *PNAS* | https://doi.org/10.1073/pnas.2318455121 |
| Silencing initiation and propagation | Silencers recruit Sir proteins via ORC/Rap1/Abf1/Sum1; iterative Sir2 deacetylation and Sir3/Sir4 binding across adjacent hypoacetylated nucleosomes propagate the domain; current expert view emphasizes probabilistic, dynamic, domain-wide cooperativity rather than static occupancy (pqac-00000009, pqac-00000010) | Review of genetic, chromatin, and live-cell evidence | Dhillon & Kamakaka 2024, *Epigenetics & Chromatin* | https://doi.org/10.1186/s13072-024-00553-7 |
| Heterochromatin bistability | A 2024 HMR model/validation study supports two-way feedback between chromatin compaction and histone modification state: compaction promotes SIR binding, which removes activating marks and drives further compaction, explaining bistable silent vs expressed states (pqac-00000011) | Theory plus experimental validation at HMR | Miangolarra et al. 2024, *PNAS* | https://doi.org/10.1073/pnas.2403316121 |
| Subtelomeric Sir3 occupancy extent | Stable, high-density Sir3 occupancy is concentrated about ±2 kb around subtelomeric SIR nucleation sites; ChIP-seq falls to background by ~4 kb downstream of XCS, but transient low-density contacts extend to ~30 kb (pqac-00000013, pqac-00000015) | Nanopore-MetID (Sir3Dam/EcoG2), ChIP-seq | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Genome-wide transient contacts | Sir3 makes contacts with >1,000 euchromatic genes; 1,197 genes (~19% of genes) were identified as Sir3 contacts; at least 15% of promoters and 7% of CDS had non-zero Sir3Dam methylation probability (pqac-00000013, pqac-00000015, pqac-00000016) | Nanopore-MetID genome-wide mapping | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Contact frequency vs distance from telomeres | ~50% of genes within 0–20 kb of subtelomeric nucleation sites are contacted by Sir3, dropping to ~20% in the next 20 kb and remaining ~20% farther toward centromeres; similarly, ~50% of genes within 20 kb of telomere ends are contacted, dropping to ~20% beyond 50 kb (pqac-00000014, pqac-00000015) | Nanopore-MetID positional analysis | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Methylation density readout for Sir3 contacts | Sir3EcoG2 methylated ~0.08% of adenines genome-wide (~6,000 A/genome); methylation near XCS averaged ~0.45%, at Yp ~0.4%, and even at HML/HMR was not >1.5%; signal dropped to ~0.1% at 4–15 kb and ~0.02% farther away (pqac-00000013, pqac-00000015) | Nanopore-MetID with adenine methylation readout | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Fraction of cells with Sir3 contact | Yp and XCS nucleation sites were methylated in ~72% of cells; high-density binding around nucleation sites occurred in ~70% of cells, whereas distal transient contacts up to ~30 kb were present in ~10–20% of cells and at ~5-fold lower density (pqac-00000013, pqac-00000015) | Single-molecule/nanopore contact frequency inference | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Sir2/Sir4 dependence of Sir3 chromatin contacts | Subtelomeric Sir3 methylation is abolished in *sir2Δ* and reduced about 2-fold in *sir4Δ*, consistent with Sir3 acting within the Sir2/3/4 complex (pqac-00000015) | Nanopore-MetID in mutant backgrounds | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Sir3 exchange dynamics | During growth arrest, Sir3 exchange is slow; after nutrient repletion, exchange and degradation increase sharply, and Sir3 bound at subtelomeric and HM loci is largely replaced by newly synthesized Sir3 by the end of the first cell cycle after release (pqac-00000008, pqac-00000014, pqac-00000016) | RITE tag-switch, ChIP-seq, nutrient-shift experiments | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Effect of reduced Sir3 supply on silencing | In a Sir3 hypomorph, SIR-dependent silencing after exit from arrest was 15–30× less efficient, and in mid-log cells 200–500× less efficient than WT; ON rates scaled with Sir3 dosage whereas OFF rates were similar (pqac-00000014) | RITE hypomorph plus silencing assays | Radman-Livaja et al. 2023, Research Square preprint | https://doi.org/10.21203/rs.3.rs-3495250/v1 |
| Magnitude of repression at HM loci | Sir-dependent repression at HML/HMR reduces transcription by roughly four orders of magnitude (~10^4-fold), while Sir proteins subsequently occupy nucleosomes across these loci (pqac-00000018) | CRASH reporter context and prior silencing literature synthesis | Fouet & Rine 2023, *Genetics* | https://doi.org/10.1093/genetics/iyac180 |
| Frequency of transient silencing loss | Using the sensitive CRASH assay, transient silencing failures at HML occurred at about 10^-3 per generation, showing that Sir-based repression is strong but not absolute (pqac-00000018) | CRASH recombinase assay at HML | Fouet & Rine 2023, *Genetics* | https://doi.org/10.1093/genetics/iyac180 |
| Gene-specific differences within a silent locus | Silencing loss at the HML α2 reporter was ~10-fold higher than at α1; when unsilenced, CRE expression was ~8-fold higher for α2 than α1, and RT-qPCR in WT showed a smaller ~4-fold difference, indicating transient failure can be gene-specific rather than locus-wide (pqac-00000017, pqac-00000018) | CRASH reporters and RT-qPCR | Fouet & Rine 2023, *Genetics* | https://doi.org/10.1093/genetics/iyac180 |


*Table: This table summarizes core mechanistic and quantitative findings for budding yeast Sir3/SIR3 (P06701), emphasizing structural nucleosome recognition, histone-mark dependencies, silencing dynamics, and 2023–2024 measurements of chromatin contacts and silencing escape.*