Yeast Epigenetics & Histone Inheritance

MATURE BIOLOGY_DOMAINFLAGSHIP

Species: yeast

Genes: GCN5 ESA1 SAS2 SAS3 RPD3 HDA1 HST1 HST2 SIR2 SIR3 SIR4 ORC1 SET1 DOT1 SPT16 POB3 ASF1 RTT109 SWI1 SWI2 SWI3 SNF5 CHD1 RCO1 PHD1

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. 25 of them
now have reviews, covering 1,255 existing annotations: 778 ACCEPT, 288
KEEP_AS_NON_CORE, 132 REMOVE, 30 MARK_AS_OVER_ANNOTATED, 11 MODIFY and 16
UNDECIDED. Most removals (110 of 132) are generic protein binding
(GO:0005515) rows; the substantive corrections were the SAS2 and SAS3
substrate specificities and a mis-filed HST1 review that was in fact ZDS1.
Two gaps remain. The CAF-1 chromatin assembly factor, whose subunits are
RLF2 (alias CAC1), CAC2 and MSI1, has no reviews yet; these are pending. (A
folder formerly named genes/yeast/CAF1/ held the unrelated CCR4-NOT
deadenylase, now renamed POP2; it is not part of this project.) CLR4 is a
fission yeast gene with no S. cerevisiae review. 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 "29 genes" and per-phase counts in the Progress section below come from
the December 2025 run and predate later re-reviews; the numbers above 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 & Demethylases - SET domain proteins
  5. Chromatin Remodelers - SWI/SNF, ISWI, CHD1, INO80 complexes
  6. Histone Chaperones - FACT, CAF-1 (RLF2/CAC1, CAC2, MSI1), ASF1 (histone recycling and deposition)
  7. Silent Chromatin & Heterochromatin - SIR proteins, H3K9 methylation (mating type locus, rDNA)
  8. Memory-Driving Mechanisms - Self-perpetuating histone modifications and feedback loops

Biological Significance

Project Goals

STATUS

Last updated: 2026-08-12

Genes to Review

Histone Acetyltransferases (HATs)

Histone Deacetylases (HDACs)

Silent Chromatin & SIR Proteins

Histone Methyltransferases & Methylation

Histone Chaperones & Recycling (FACT Complex & Associated)

Histone Modifications - Readers & Adaptors

Progress

PROJECT COMPLETE: 29/29 genes (100%)

COMPLETE PROJECT TOTALS:
- Total genes: 29 | Total annotations: 1,310 | ACCEPT: 866 (66.1%)

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
- Excellence: H3K4me3 reader, independent chromatin remodeler (not SWI/SNF member)
- 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 - H3K4me3 reader)
- 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: H3K4me3 recognition, Rpd3S complex component, 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

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

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)

2025-12-30

Slides