Yeast Epigenetics & Histone Inheritance

Bottom line: budding yeast keeps silent and active chromatin states
through cell division with a small set of histone writers, erasers, readers,
chaperones and remodelers. We planned reviews of S. cerevisiae genes in
those classes (acetyltransferases, deacetylases, SIR silencing proteins,
methyltransferases, FACT and other chaperones, SWI/SNF and CHD1, and the
Rpd3S reader RCO1) to test how well GO captures their chromatin functions. All
28 intended S. cerevisiae genes now have reviews, covering 1,373 existing GO
annotations plus 11 proposed NEW rows: 828 ACCEPT, 184 KEEP_AS_NON_CORE, 305
REMOVE, 22 MODIFY, 19 MARK_AS_OVER_ANNOTATED and 15 UNDECIDED. Most removals
(270 of 305) are generic protein binding (GO:0005515) rows; the substantive
corrections include SAS2 and SAS3 substrate specificities, SIR/ORC functional
separation, SWI/SNF DNA-binding and structural-subunit overcalls, and a
mis-filed HST1 review that was in fact ZDS1. The CAF-1 chromatin assembly
factor is now represented by RLF2 (alias CAC1), CAC2 and MSI1. CLR4, an
early checklist entry, has been dropped from scope: it is the fission yeast
H3K9 methyltransferase, and budding yeast has neither H3K9 methylation nor a
Clr4/SUV39 ortholog, so there is no S. cerevisiae gene to substitute for it
(its fission yeast review is SCHPO/clr4). PHD1, filed below as a histone
reader, is not one: the name means "pseudohyphal determinant", it has no PHD
finger, and its review describes an APSES-family transcription factor that
controls pseudohyphal growth.

The dated notes below are retained for provenance and predate later re-reviews;
the manifest and Progress section are recounted from the current review files.

Overview

This project reviews Saccharomyces cerevisiae genes central to epigenetic memory, histone modification dynamics, and histone inheritance through cell division. Yeast serves as the premier model for understanding how chromatin states persist across generations of cells despite the challenges of DNA replication. Recent cryo-EM structures reveal how the FACT complex captures parental histones during replication to maintain epigenetic inheritance.

Key Research Areas

1. Histone Modifications - Acetylation, methylation, phosphorylation and writers/readers/erasers
2. Histone Acetyltransferases (HATs) - GCN5, ESA1, Sas family
3. Histone Deacetylases (HDACs) - Rpd3, Hda1, sirtuins (SIR2/HST family)
4. Histone Methyltransferases - Set1 and Dot1 writers for H3K4 and H3K79 methylation
5. Chromatin Remodelers - SWI/SNF and CHD1 remodelers
6. Histone Chaperones - FACT, CAF-1 (RLF2/CAC1, CAC2, MSI1), ASF1 (histone recycling and deposition)
7. Silent Chromatin & Heterochromatin - SIR proteins and Sir2 silencing at HM loci, telomeres, and rDNA
8. Memory-Driving Mechanisms - Self-perpetuating histone modifications and feedback loops

Biological Significance

• Epigenetic inheritance - Non-genetic information transfer through cell divisions
• Disease models - Histone mutations and modifications linked to cancer, neurodegeneration
• Chromatin memory - Understanding cellular state maintenance and cell identity
• Structural biology - Recent cryo-EM revealing histone-DNA interactions and FACT dynamics
• Therapeutic potential - HDAC inhibitors and other epigenetic drugs
• Gene regulation - How histone modifications control gene expression globally

Project Goals

• Review genes controlling histone modifications and chromatin states
• Assess GO annotations for epigenetic functions and histone dynamics
• Incorporate structural insights into histone recycling and FACT mechanisms
• Identify genes maintaining silent chromatin and heterochromatin
• Create reference for epigenetics and histone biology research

STATUS

Last updated: 2026-10-16

Genes to Review

Histone Acetyltransferases (HATs)

• Done: GCN5 - General control non-repressed (HAT, Gen5p/Gcn5p)
• Done: ESA1 - Essential SAS-related (KAT5 homolog, NuA4 complex)
• Done: SAS2 - Something about silencing 2 (SAS complex H4K16 acetyltransferase)
• Done: SAS3 - Something about silencing 3 (NuA3 complex H3K14 acetyltransferase)

Histone Deacetylases (HDACs)

• Done: RPD3 - Reduced potassium dependency (HDAC, class I)
• Done: HDA1 - Histone deacetylase (HDAC, class II)
• Done: HST1 - Histone deacetylase sirtuin (NAD+-dependent, class III)
• Done: HST2 - Histone deacetylase sirtuin (NAD+-dependent)
• Done: SIR2 - Silent information regulator (NAD+-dependent deacetylase, master regulator)

Silent Chromatin & SIR Proteins

• Done: SIR3 - Silent information regulator (Sir3p, components silent chromatin)
• Done: SIR4 - Silent information regulator (Sir4p, components silent chromatin)
• Done: ORC1 - Origin recognition complex (SIR complex targeting)

Histone Methyltransferases & Methylation

• Done: SET1 - Histone methyltransferase (H3K4 methylation, COMPASS complex)
• Done: DOT1 - Disruptor of telomeric silencing (H3K79 methyltransferase)
• Dropped: CLR4 - fission yeast H3K9 methyltransferase; S. cerevisiae has no H3K9 methylation and no Clr4/SUV39 ortholog, so no budding yeast replacement was added
• Future work: SET2 (H3K36 methyltransferase) is not yet reviewed; it is not a Clr4 substitute, but its H3K36me mark is read (via Eaf3) by Rpd3S, the complex of in-scope RCO1

Histone Chaperones & Recycling (FACT Complex & Associated)

• Done: SPT16 - Facilitates chromatin transcription (FACT component, H2A/H2B transfer)
• Done: POB3 - Promoter of basal transcription (FACT component, SSRP1 homolog)
• Done: RLF2 (alias CAC1) - CAF-1 large subunit (H3/H4 deposition)
• Done: CAC2 - CAF-1 subunit
• Done: MSI1 - CAF-1 subunit (WD40, RbAp48 homolog)
• Done: ASF1 - Anti-silencing function protein (H3/H4 chaperone)
• Done: RTT109 - H3K56 acetyltransferase (newly synthesized histone acetylation)

Chromatin Remodelers (SWI/SNF & Related)

• Done: SWI1 - Switch 1 (SWI/SNF complex regulatory subunit)
• Done: SWI2 - Switch 2 (SWI/SNF complex ATPase)
• Done: SWI3 - Switch 3 (SWI/SNF complex regulatory subunit)
• Done: SNF5 - Sucrose nonfermenting (SWI/SNF complex)
• Done: CHD1 - Chromatin helicase DNA-binding (nucleosome remodeler)

Histone Modifications - Readers & Adaptors

• Done: RCO1 - Regulator of chromatin organization (Rpd3S unmodified-H3-tail reader)
• Done: PHD1 - Pseudohyphal determinant; APSES transcription factor (not a histone reader, despite the name)

Progress

CURRENT REVIEW TOTALS: 28/28 intended S. cerevisiae genes reviewed

• Phase 1 (HATs): 4/4 genes - 197 existing annotations, 118 ACCEPT
• Phase 2 (HDACs): 5/5 genes - 330 existing annotations, 185 ACCEPT
• Phase 3 (Silent Chromatin): 3/3 genes - 130 existing annotations, 80 ACCEPT
• Phase 4 (HMTs): 2/2 yeast genes - 109 existing annotations, 76 ACCEPT
• Phase 5 (Histone Chaperones): 7/7 genes - 308 existing annotations, 177 ACCEPT
  • CAF-1 is now covered by RLF2/CAC1, CAC2 and MSI1.
• Phase 6 (Chromatin Remodelers): 5/5 genes - 257 existing annotations, 169 ACCEPT
  • SWI1: 40 existing annotations, plus 1 proposed NEW row
  • SWI2: 76 existing annotations
  • SWI3: 40 existing annotations
  • SNF5: 36 existing annotations
  • CHD1: 65 existing annotations
• Phase 7 (RCO1 reader + PHD1 TF): 2/2 genes - 42 existing annotations, 23 ACCEPT
  • RCO1: 29 existing annotations, plus 1 proposed NEW row
  • PHD1: 13 existing annotations

Current aggregate totals:

• Total reviewed rows: 1,384 | Existing annotations: 1,373 | Proposed NEW rows: 11 | ACCEPT: 828

NOTES

2025-12-31 (PROJECT COMPLETION - Phases 6 & 7)

Phase 6 - Chromatin Remodelers (SWI1, SWI2, SWI3, SNF5, CHD1)

SWI1 (Switch 1 - SWI/SNF ATPase)

• 40 annotations → 17 ACCEPT (42.5%), 19 KEEP_AS_NON_CORE, 1 REMOVE
• Key finding: Removed incorrect "transcription cis-regulatory region binding" annotation
• Core: SWI/SNF complex membership, nucleosome remodeling, transcriptional activation

SWI2 (Switch 2 / SNF2 - SWI/SNF helicase ATPase)

• 76 annotations → 52 ACCEPT (68.4%), 23 KEEP_AS_NON_CORE, 1 OVER_ANNOTATED
• Excellence: Primary catalytic ATPase with strong experimental evidence
• Core: ATP hydrolysis, helicase activity, nucleosome repositioning, RNA Pol II activation

SWI3 (Switch 3 - SWI/SNF scaffold)

• 40 annotations → 18 ACCEPT (45%), 16 KEEP_AS_NON_CORE, 4 REMOVE
• Critical correction: Removed 4 incorrect DNA binding annotations (SWIRM domain is protein-interaction, not DNA-binding)
• Core: SWI/SNF complex assembly, chromatin remodeling coordination, transcriptional regulation

SNF5 (Sucrose nonfermenting 5 - SWI/SNF regulatory subunit)

• 36 annotations → 20 ACCEPT (55.6%), 10 KEEP_AS_NON_CORE
• Key role: Histone acetylation sensing, tumor suppressor-like function
• Core: SWI/SNF assembly, transcriptional regulation, complex targeting

CHD1 (Chromatin helicase DNA-binding 1)

• 65 annotations → 52 ACCEPT (80%), 11 KEEP_AS_NON_CORE, 2 OVER_ANNOTATED
• Caveat: direct yeast CHD1 H3K4me3-reader activity was later moved to UNDECIDED; core CHD1 biology is ATP-dependent nucleosome sliding/spacing and transcription-coupled chromatin restoration
• Core: ATP-dependent nucleosome remodeling, histone methylation recognition, transcription initiation/elongation

Phase 6 Summary: 257 annotations, 159 ACCEPT (61.9%), reveals SWI/SNF complex annotation heterogeneity

Phase 7 - Histone Reader RCO1, plus PHD1 (APSES TF, mis-filed here)

RCO1 (Regulator of Chromatin Organization 1 - Rpd3S H3-tail reader/adaptor)

• 28 annotations → 11 ACCEPT (39.3%), 13 KEEP_AS_NON_CORE, 1 MODIFY
• Challenge: Lowest ACCEPT rate due to pleiotropic and indirect functions
• Modification: GO:0006357 too broad - should be "chromatin organization" or "antisense regulation"
• Core: unmodified-H3-tail/H3K4me0 readout, Rpd3S complex assembly, cryptic transcription suppression

PHD1 (Pseudohyphal Determinant 1 - APSES transcription factor; no PHD finger, not a histone reader)

• 13 annotations → 11 ACCEPT (84.6%), 2 KEEP_AS_NON_CORE
• Excellence: Highest ACCEPT rate in Phase 7, well-characterized master regulator
• Core: Sequence-specific DNA binding, positive transcription regulation, pseudohyphal growth regulation

Phase 7 Summary: 41 annotations, 22 ACCEPT (54%), master regulatory functions in developmental control

Project-Wide Insights

Annotation Quality by Gene Type:

• Single-function enzymes (HDACs, methyltransferases): 70-84% ACCEPT
• Multi-subunit complexes (SWI/SNF, FACT): 55-65% ACCEPT
• Histone chaperones (ASF1, RTT109): 47-81% ACCEPT
• Phase 7 (reader RCO1; PHD1 is an APSES TF, not a reader): 39-85% ACCEPT
• Chromatin remodelers (CHD1, SWI2): 68-80% ACCEPT

Common Annotation Issues Across All Phases:

1. Generic "protein binding" (IPI) - 189 instances (14.4% of all annotations)
2. Over-generalization of parent terms vs. specific child terms
3. Incorrect domain-to-function inferences
4. Complex-level vs. subunit-level annotation confusion
5. Context-dependent functional annotations treated as universal

Corrective Actions Implemented:

• Removed 16 incorrect annotations (DNA binding, substrate misidentification)
• Marked 394 generic annotations as non-core (functional but uninformative)
• Proposed 6 modifications for better term choices
• Flagged 8 annotations as undecided pending additional evidence

2025-12-31 (Phase 4 & 5 Completion)

Phase 4 - Histone Methyltransferases (SET1, DOT1)

SET1 (Histone-lysine N-methyltransferase, H3 lysine-4 specific)

• 68 total annotations → 45 ACCEPT (66.2%), 22 KEEP_AS_NON_CORE (32.4%)
• Core functions: H3K4 methylation (mono/di/tri-methylation), COMPASS complex component, transcriptional regulation
• Key findings: Well-characterized histone methyltransferase with strong experimental evidence across all major annotation categories
• Evidence quality: 54% from experimental studies (IMP, IDA, IGI), 46% from computational/phylogenetic inference

DOT1 (Disruptor of Telomeric Silencing 1 - H3K79 methyltransferase)

• 41 total annotations → 31 ACCEPT (75.6%), 5 KEEP_AS_NON_CORE (12.2%), 1 REMOVE (2.4%), 4 OVER_ANNOTATED (9.8%)
• Core functions: H3K79 methylation (specific for H3K79, not promoter-associated), DNA damage checkpoint signaling, transcriptional regulation
• Key finding: Removed generic "protein binding" annotation (GO:0005515) violating GO guidelines for uninformative terms
• Evidence quality: 54% experimental, comprehensive genetic characterization from multiple laboratories

Phase 4 Summary: 109 annotations total, 76 ACCEPT (69.7%), exceptionally well-characterized methyltransferases with high annotation quality

Phase 5 - Histone Chaperones & Histone Modifiers (SPT16, POB3, ASF1, RTT109)

SPT16 (FACT complex subunit - H2A/H2B histone chaperone)

• 56 total annotations → 30 ACCEPT (53.6%), 26 KEEP_AS_NON_CORE (46.4%)
• Core functions: Nucleosome disassembly/assembly, FACT complex component, transcription elongation facilitation
• Challenge: 14 generic "protein binding" annotations obscure specific histone/nucleosome interactions
• Key insight: FACT works as obligate SPT16-POB3 heterodimer; histone transfer and nucleosome dynamics are primary functions

POB3 (FACT complex subunit - stabilizing partner)

• 32 total annotations → 18 ACCEPT (56.3%), 11 KEEP_AS_NON_CORE (34.4%), 1 OVER_ANNOTATED (3.1%), 2 UNDECIDED (6.3%)
• Core functions: FACT complex assembly (structural component), nucleosome dynamics, DNA replication
• Limitation: Less individually characterized than SPT16; many annotations reflect shared FACT complex function
• Key finding: POB3 provides stabilization but NOT histone chaperone activity like SPT16

ASF1 (Histone chaperone - H3/H4 dimer handler)

• 47 total annotations → 22 ACCEPT (46.8%), 24 KEEP_AS_NON_CORE (51.1%), 1 OVER_ANNOTATED (2.1%)
• Core functions: H3/H4 dimer chaperone (distinct from FACT's H2A/H2B), replication-dependent nucleosome assembly, transcription-coupled recycling
• Challenge: Lowest ACCEPT rate (47%) due to pleiotropic roles and overlap with multiple functional partners
• Key insight: Hub protein interacting with CAF-1, FACT, RTT109, SIR proteins; central to epigenetic memory maintenance

RTT109 (H3K56 Acetyltransferase)

• 70 total annotations → 57 ACCEPT (81.4%), 12 KEEP_AS_NON_CORE (17.1%), 1 OVER_ANNOTATED (1.4%)
• Core function: H3K56 acetyltransferase on newly synthesized (non-nucleosomal) histones - unique among HATs
• Excellence: Highest ACCEPT rate (81.4%) across all Phase 5 genes; exceptionally well-characterized with 8 crystal structures
• Evidence quality: 8 crystal structures + comprehensive biochemical characterization + genetic validation

Phase 5 Summary: 205 annotations across 4 genes, 127 ACCEPT (61.9%), reveals complexity of histone chaperone network and generic annotation over-representation

Deep Research Completion

• All 6 genes (SET1, DOT1, SPT16, POB3, ASF1, RTT109) have Perplexity deep research files (a seventh, filed under CAF1, was for the POP2 deadenylase, not the chromatin assembly factor)
• Cyberian (Claude) deep research encountered technical issues - Perplexity research sufficient for comprehensive reviews
• Research files available in each gene folder: *-deep-research-perplexity.md

Key Insights Across Phases 4-5

1. Histone methyltransferases show high quality annotations (70% ACCEPT) - well-established specificity
2. FACT complex annotations reveal tension between complex-level vs. protein-level functions (55% ACCEPT)
3. Histone chaperone network is highly interconnected with multiple functional overlaps (62% ACCEPT)
4. Generic protein binding annotations systematically over-represented in chaperone proteins (50+ instances)
5. Newly-synthesized histone modifications (RTT109 H3K56ac) are distinct from chromatin-incorporated modifications

Issues Identified & Notes

• CAF1 nomenclature collision (resolved): the folder named "CAF1" held POP2 (CCR4-NOT mRNA deadenylase, P39008), not the chromatin assembly factor; it was renamed genes/yeast/POP2/ (PR #3236). The CAF-1 histone chaperone subunits RLF2 (CAC1), CAC2 and MSI1 now have separate reviews
• SAS2/SAS3 substrate corrections: Successfully corrected project description errors (H3K9 → H4K16/H3K14)
• HST1 nomenclature error corrected and canonical review completed: P50111/YMR273C is the PP2A-Cdc55 regulator ZDS1, not the sirtuin HST1; its review was moved to genes/yeast/ZDS1/. Canonical HST1 (P53685/YOL068C) now has a separate literature-backed review.

2025-12-31

Phase 3 Completion Summary

ORC1 (Origin Recognition Complex subunit 1)

• 48 total annotations (subset duplicates with different evidence codes)
• 28 ACCEPT (58%) - core ORC1 functions
• 20 KEEP_AS_NON_CORE (42%) - mechanically correct but less informative
• 0 REMOVE - high quality annotation set
• Key findings:
  • DNA replication origin binding (GO:0003688) confirmed core function
  • Silent mating-type cassette heterochromatin formation (GO:0030466) well-supported by IDA/IGI evidence
  • ORC1 has dual roles in both DNA replication and SIR-mediated silencing
  • BAH domain enables nucleosome binding (GO:0031491, GO:0034728)
  • Validation: PASSED

Phase 1-2 Summary

Phase 1 - Histone Acetyltransferases (HATs)

• GCN5: 69 annotations → 40 ACCEPT (58%)
• ESA1: 63 annotations → 29 ACCEPT (46%)
• SAS2: 27 annotations → 17 ACCEPT (63%) - corrected substrate specificity (H4K16, not H3K9)
• SAS3: 38 annotations → 21 ACCEPT (55%) - corrected substrate specificity (H3K14, not H3K9)

Phase 2 - Histone Deacetylases (HDACs)

• RPD3: 160 annotations → 85 ACCEPT (53%)
• HDA1: 38 annotations → 27 ACCEPT (71%)
• ZDS1 (formerly misfiled as HST1): 27 consolidated review entries → 9 ACCEPT,
  11 KEEP_AS_NON_CORE, 7 MARK_AS_OVER_ANNOTATED. The corrected review retains
  direct ZDS1 evidence for PP2A-Cdc55 inhibition and secondary heterochromatin effects,
  and synthesizes a PP2A-Cdc55 spatial-regulation core function; these
  results do not represent the sirtuin HST1.
• HST1 (canonical P53685/YOL068C): 38 annotations → 15 ACCEPT, 8 KEEP_AS_NON_CORE, 11 MARK_AS_OVER_ANNOTATED, 2 REMOVE, 2 UNDECIDED. The review distinguishes native Sum1-Rfm1-Hst1 promoter repression from conditional Sum1-1 mating-type silencing and rejects Sir2-derived telomeric inferences.
• HST2: 26 annotations → 21 ACCEPT (81%)
• SIR2: 79 annotations → 50 ACCEPT (63%)

Critical Corrections Made

1. SAS2/SAS3 substrate specificity: Corrected from H3K9 to H4K16/H3K14
2. HST1 nomenclature and function: Identified P50111/YMR273C as ZDS1, then reviewed canonical HST1/P53685 as a locus-specific NAD-dependent deacetylase whose main context is the Sum1-Rfm1-Hst1 repressor rather than Sir2-like regional silencing
3. Generic protein binding annotations: Systematically marked as non-core
4. Phylogenetic inference errors: Corrected SAS2 complex assignment

Next Phases (4-7)

• Phase 4: Histone Methyltransferases (SET1, DOT1; CLR4 dropped as a fission yeast gene)
• Phase 5: Histone Chaperones & FACT (SPT16, POB3, CAF-1 [RLF2, CAC2, MSI1], ASF1, RTT109)
• Phase 6: Chromatin Remodelers (SWI1, SWI2, SWI3, SNF5, CHD1)
• Phase 7: Histone Reader RCO1 (PHD1 is an APSES TF, not a reader)

2025-12-30

• Project initialized
• Focus: histone modifications, epigenetic inheritance, histone recycling during replication
• Selected 29 genes spanning HATs, HDACs, SIR proteins, histone methyltransferases, and histone chaperones
• Emphasis on FACT complex dynamics and structural biology of histone inheritance
• Ready to begin gene review workflow