Histone acetyltransferase RTT109 (also KAT11, Regulator of Ty1 transposition protein 109) catalyzes acetylation of newly synthesized histone H3 at lysines 56, 9, 27, 14, and 23 in coordination with histone chaperone cofactors Vps75 and Asf1. RTT109 is absolutely essential for replication-dependent nucleosome assembly and genome stability, as H3K56ac marks nascent DNA and facilitates proper chromatin assembly while preventing double-strand break formation. RTT109 also prevents DNA-RNA hybrid accumulation through H3K14 and H3K23 acetylation. The enzyme exhibits a unique bipartite architecture with N-terminal PAT domain and C-terminal activation domain, undergoes autoacetylation at K290 for catalytic activation, and functions exclusively on newly synthesized non-nucleosomal histones during S-phase replication.
Definition: Any process that decreases the rate, frequency, or extent of R-loop (DNA-RNA hybrid) formation, for example by a chromatin state or histone modification that renders the DNA template less permissive to hybridization with nascent RNA.
Justification: RTT109 loss increases cellular R-loop/DNA-RNA hybrid levels via loss of H3K14 and H3K23 acetylation (PMID:35866610), a function distinct from its defining H3K56ac role in replication-coupled nucleosome assembly and from its separate role in repairing R-loop-associated DNA breaks. No existing GO term captures formation-prevention specifically; the only R-loop process term, GO:0062176 (R-loop processing), is defined as R-loop disassembly, the opposite direction of effect. The mechanism here is chromatin-based β H3K14/H3K23 acetylation rendering the template less permissive to DNA-RNA hybridization β but chromatin organization is the mechanism rather than the parent class. Because the term being proposed is a negative-regulation class, it is parented under GO:0051053 (negative regulation of DNA metabolic process), the nearest existing negative-regulation ancestor, R-loop processing being itself classified in GO as a DNA metabolic process.
Parent term: negative regulation of DNA metabolic process
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0032931 histone H3K56 acetyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: H3K56 acetyltransferase activity is RTT109 core defining function Reason: RTT109 is sole acetyltransferase for H3K56 on newly synthesized histones. Essential for genome stability - rtt109Ξ shows 3-4 fold elevated spontaneous DSBs and 9-fold higher gross chromosomal rearrangements. Supported by 8 crystal structures revealing active site and multiple biochemical studies. Supporting Evidence: PMID:18707894 Saccharomyces cerevisiae Rtt109 is an important class of histone acetyltransferases (HATs), which promote genome stability by directly acetylating newly synthesized histone H3 lysine 56 (H3-K56) through an unknown mechanism file:yeast/RTT109/RTT109-deep-research-perplexity.md See deep research file for comprehensive analysis file:yeast/RTT109/RTT109-deep-research-falcon.md In budding yeast, its defining and dominant reaction is acetylation of **histone H3 lysine 56 (H3K56ac)** file:yeast/RTT109/RTT109-deep-research-falcon.md Loss of RTT109 causes βabsence of detectable K56 acetylationβ in vivo, establishing Rtt109 as essential for H3K56ac |
| GO:0006974 DNA damage response | IBA GO_REF:0000033 | ACCEPT | Summary: DNA damage response through H3K56 acetylation in replication Reason: RTT109 essential for S-phase genome stability. rtt109Ξ cells display 3-4 fold elevated spontaneous DNA damage, severe hypersensitivity to genotoxic agents (MMS, HU, CPT), and impaired nucleosome reassembly at damage sites. Supporting Evidence: file:yeast/RTT109/RTT109-deep-research-falcon.md In a foundational *Science* study, **rtt109\u0394** caused an approximately **9\u2011fold increase in gross chromosomal rearrangement** frequency and showed phenotypes consistent with replication-associated DNA damage tolerance defects file:yeast/RTT109/RTT109-deep-research-falcon.md rtt109\u0394 eliminates H3K56ac and is epistatic with H3K56R for HU sensitivity, placing Rtt109 upstream of the H3K56ac-dependent replication stress response |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: RTT109 localizes to nucleus for replication and chromatin functions Reason: Nucleus is essential cellular compartment for RTT109 acetyltransferase function in DNA replication and nucleosome assembly. Nuclear localization mediated by Vps75 histone chaperone. Supporting Evidence: file:yeast/RTT109/RTT109-deep-research-falcon.md Newly synthesized H3βH4 are escorted toward the nucleus by chaperone pathways, with Rtt109 acting in complex with Asf1 to acetylate H3K56, linking the reaction to replication-coupled chromatin assembly file:yeast/RTT109/RTT109-deep-research-falcon.md H3K56 acetylation is required for S-phase chromosome domain positioning (e.g., telomere peripheral localization), reinforcing that the functional action is on nuclear chromatin during/after replication |
| GO:0004402 histone acetyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: General histone acetyltransferase activity. The crystal structure of Rtt109 in complex with acetyl-CoA (PDB 3CZ7; Stavropoulos et al. 2008) shows a core PAT domain that binds the acetyl-CoA cofactor and is responsible for acetylating H3K56. Reason: Broad classification encompassing H3K56, K9, K27, K14, K23 acetyltransferase activities on newly synthesized histones. Supporting Evidence: PMID:18719104 Rtt109 is a protein acetyltransferase (PAT) that is responsible for the acetylation of lysine-56 of histone 3 (H3K56) in yeast. PMID:18719104 Here, we present the crystal structure of Rtt109 in complex with acetyl-CoA at a 2.0-A resolution. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Nuclear localization for DNA replication functions Reason: RTT109 functions in nucleus during S-phase DNA replication and chromatin assembly. |
| GO:0006325 chromatin organization | IEA GO_REF:0000002 | ACCEPT | Summary: RTT109 controls chromatin organization through H3K56 acetylation Reason: H3K56 acetylation creates relaxed chromatin structure on nascent DNA during replication and facilitates proper nucleosome positioning and assembly. Multiple biochemical studies confirm chromatin structural changes. |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000043 | ACCEPT | Summary: RTT109 involved in DNA-templated transcription through transcriptional buffering Reason: H3K56 acetylation suppresses transcription from newly replicated loci during S-phase, maintaining expression homeostasis despite doubling of genomic DNA. This is secondary transcriptional regulation function. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: Regulation of DNA-templated transcription during replication Reason: RTT109 suppresses transcription at early-replicating genes through H3K56 acetylation, preventing transcriptional upregulation proportional to DNA content increase. |
| GO:0006974 DNA damage response | IEA GO_REF:0000043 | ACCEPT | Summary: DNA damage response annotation consistent with S-phase genome stability role Reason: RTT109 enables cellular response to DNA damage by acetylating H3K56, promoting nucleosome assembly and preventing spontaneous double-strand break formation. |
| GO:0010484 histone H3 acetyltransferase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Histone H3 acetyltransferase activity. The 2.0-A crystal structure of Rtt109 bound to acetyl-CoA (PDB 3CZ7) confirms it is the acetyltransferase responsible for H3K56 acetylation. Reason: RTT109 catalyzes acetylation of histone H3 at multiple lysine residues (K56, K9, K27, K14, K23) depending on histone chaperone cofactor. Supporting Evidence: PMID:18719104 Rtt109 is a protein acetyltransferase (PAT) that is responsible for the acetylation of lysine-56 of histone 3 (H3K56) in yeast. PMID:18719104 Here, we present the crystal structure of Rtt109 in complex with acetyl-CoA at a 2.0-A resolution. |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: General transferase activity too broad Reason: Transferase activity (GO:0016740) is extremely broad classification encompassing tens of thousands of enzymes. More specific child terms already annotated (protein-lysine-acetyltransferase, histone acetyltransferase). While technically correct, offers minimal information value per GO guidelines. |
| GO:0061733 protein-lysine-acetyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Protein-lysine-acetyltransferase activity. The crystal structure of Rtt109 in complex with acetyl-CoA (PDB 3CZ7, ligand ACO; Stavropoulos et al. 2008) directly shows acetyl-CoA bound in the core PAT domain, the cofactor donor for lysine acetylation. Reason: RTT109 catalyzes lysine acetylation using acetyl-CoA as cofactor. EC 2.3.1.48 classification confirmed by enzymatic characterization. Supporting Evidence: PMID:18719104 Rtt109 consists of a core PAT domain, which binds the acetyl-CoA cofactor. PMID:18719104 Here, we present the crystal structure of Rtt109 in complex with acetyl-CoA at a 2.0-A resolution. |
| GO:0005515 protein binding | IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... | KEEP AS NON CORE | Summary: RTT109 binds Vps75 histone chaperone Reason: RTT109 forms essential physical complex with Vps75 which activates H3K56 acetyltransferase activity 100-fold. Generic protein binding term does not convey specificity - Vps75 serves critical catalytic activation role. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. |
| GO:0005515 protein binding | IPI PMID:17314980 Functional dissection of protein complexes involved in yeast... | KEEP AS NON CORE | Summary: RTT109 protein interaction with Vps75 Reason: Documents direct physical interaction between RTT109 and Vps75 histone chaperone cofactor. Supporting Evidence: PMID:17314980 Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. |
| GO:0005515 protein binding | IPI PMID:18723682 Structure of Vps75 and implications for histone chaperone fu... | KEEP AS NON CORE | Summary: RTT109 protein interaction with Vps75 Reason: Multiple IPI entries document robust, well-characterized Vps75 interaction. Supporting Evidence: PMID:18723682 Structure of Vps75 and implications for histone chaperone function. |
| GO:0005515 protein binding | IPI PMID:19172748 Molecular functions of the histone acetyltransferase chapero... | KEEP AS NON CORE | Summary: RTT109 interacts with Vps75 Reason: Direct protein-protein interaction documented across multiple studies. Supporting Evidence: PMID:19172748 Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. |
| GO:0005515 protein binding | IPI PMID:19172749 Histone chaperone specificity in Rtt109 activation. | KEEP AS NON CORE | Summary: RTT109 binds Asf1 histone chaperone Reason: RTT109 interacts with Asf1 which directs substrate specificity toward H3K56 acetylation. Supporting Evidence: PMID:19172749 Histone chaperone specificity in Rtt109 activation. |
| GO:0005515 protein binding | IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome. | KEEP AS NON CORE | Summary: RTT109 interacts with Asf1 Reason: Direct interaction with Asf1 histone chaperone cofactor. Supporting Evidence: PMID:21179020 Defining the budding yeast chromatin-associated interactome. |
| GO:0005515 protein binding | IPI PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications... | KEEP AS NON CORE | Summary: RTT109 protein binding interactions documented Reason: IPI entries document protein-protein interactions with histone chaperone cofactors. Supporting Evidence: PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | KEEP AS NON CORE | Summary: Protein binding annotation Reason: Generic protein binding term for interactions with histone chaperones. Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome. |
| GO:0006325 chromatin organization | IDA PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected str... | ACCEPT | Summary: Chromatin organization through replication-dependent acetylation Reason: Direct biochemical demonstration of RTT109 role in organizing newly assembled chromatin. Supporting Evidence: PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. |
| GO:0006325 chromatin organization | IMP PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected str... | ACCEPT | Summary: Chromatin organization by RTT109-mediated histone acetylation Reason: IMP evidence: rtt109Ξ cells display disorganized chromatin at replicated regions. Supporting Evidence: PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. |
| GO:0006325 chromatin organization | IDA PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by... | ACCEPT | Summary: Chromatin organization mediated by RTT109 Reason: Direct observations of RTT109 effects on chromatin structure. Supporting Evidence: PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by Rtt109. |
| GO:0006325 chromatin organization | IDA PMID:29300933 Structural characterization of the Asf1-Rtt109 interaction a... | ACCEPT | Summary: RTT109 controls chromatin organization during replication Reason: Multiple independent studies confirm role in organizing nascent chromatin. Supporting Evidence: PMID:29300933 Structural characterization of the Asf1-Rtt109 interaction and its role in histone acetylation. |
| GO:0006325 chromatin organization | IDA PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acet... | ACCEPT | Summary: Replication-coupled chromatin organization by RTT109 Reason: H3K56 acetylation essential for proper nucleosome assembly on replicated DNA. Supporting Evidence: PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acetylation specificity. |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:19172748 Molecular functions of the histone acetyltransferase chapero... | ACCEPT | Summary: DNA replication-dependent chromatin assembly is RTT109 primary function Reason: RTT109 marks nascent DNA through H3K56 acetylation, facilitating H3-H4 transfer to CAF1 for PCNA-coupled nucleosome deposition. Essential for proper replication-dependent nucleosome assembly. Supporting Evidence: PMID:19172748 Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75 file:yeast/RTT109/RTT109-deep-research-falcon.md H3K56ac marks newly synthesized H3 during S phase and promotes binding of histone deposition factors **CAF-1** and **Rtt106**, linking Rtt109 directly to replication-coupled nucleosome assembly file:yeast/RTT109/RTT109-deep-research-falcon.md Asf1 presents H3βH4 to **Rtt109** for H3K56 acetylation |
| GO:0006335 DNA replication-dependent chromatin assembly | IDA PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications... | ACCEPT | Summary: Replication-dependent chromatin assembly mediated by H3K56 acetylation Reason: RTT109-catalyzed H3K56 acetylation essential step in RCNA pathway coordinating with replication machinery. Supporting Evidence: PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation. |
| GO:0006338 chromatin remodeling | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: Chromatin remodeling through H3K56 acetylation weakening DNA-histone contacts Reason: H3K56 acetylation weakens histone-DNA interactions, promoting nucleosome replacement ahead of replication forks and chromatin disassembly during transcription. Supporting Evidence: PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0000785 chromatin | IDA PMID:21463458 Interaction with the histone chaperone Vps75 promotes nuclea... | ACCEPT | Summary: RTT109 is component of H3 histone acetyltransferase complexes at chromatin Reason: RTT109 physically associates with Vps75 and Asf1 to form active acetyltransferase complexes that localize to chromatin. Supporting Evidence: PMID:21463458 Interaction with the histone chaperone Vps75 promotes nuclear localization and HAT activity of Rtt109 in vivo. |
| GO:0006357 regulation of transcription by RNA polymerase II | IMP PMID:19620280 Cooperation between the INO80 complex and histone chaperones... | ACCEPT | Summary: Regulation of RNA polymerase II transcription during S-phase Reason: RTT109 suppresses transcription from newly replicated genes through H3K56 acetylation, preventing transcriptional upregulation during active DNA replication. Supporting Evidence: PMID:19620280 Cooperation between the INO80 complex and histone chaperones determines adaptation of stress gene transcription |
| GO:0033554 cellular response to stress | IMP PMID:19620280 Cooperation between the INO80 complex and histone chaperones... | ACCEPT | Summary: Cellular response to DNA damage stress Reason: RTT109 enables cell survival to genotoxic stress by acetylating H3 histones, promoting nucleosome assembly and preventing DNA damage. Supporting Evidence: PMID:19620280 Cooperation between the INO80 complex and histone chaperones determines adaptation of stress gene transcription in the yeast Saccharomyces cerevisiae. |
| GO:0043992 histone H3K9 acetyltransferase activity | IMP PMID:19172748 Molecular functions of the histone acetyltransferase chapero... | ACCEPT | Summary: Histone H3K9 acetyltransferase activity mediated by Rtt109-Vps75 Reason: RTT109-Vps75 complex specifically acetylates H3K9 on newly synthesized histones. H3K9 residue in N-terminal tail region of H3. Supporting Evidence: PMID:19172748 Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. file:yeast/RTT109/RTT109-deep-research-falcon.md Mass spectrometry and enzymology implicated H3 tail lysines such as **K9** (and other tail sites) as targets of the Rtt109βVps75 complex, and VPS75 deletion reduced S-phase H3K9ac substantially file:yeast/RTT109/RTT109-deep-research-falcon.md VPS75 loss caused ~**60% reduction** in H3K9ac during S phase while having modest effect on bulk H3K56ac |
| GO:0043994 histone H3K23 acetyltransferase activity | IMP PMID:19172748 Molecular functions of the histone acetyltransferase chapero... | ACCEPT | Summary: H3K23 acetyltransferase activity Reason: RTT109 acetylates histone H3K23 residue in coordination with Vps75 on newly synthesized histones. Supporting Evidence: PMID:19172748 Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. |
| GO:0005515 protein binding | IPI PMID:21454705 Structure and histone binding properties of the Vps75-Rtt109... | KEEP AS NON CORE | Summary: RTT109 protein interaction with Vps75 Reason: Direct binding documented in multiple studies. Supporting Evidence: PMID:21454705 Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex. |
| GO:0005515 protein binding | IPI PMID:29300933 Structural characterization of the Asf1-Rtt109 interaction a... | KEEP AS NON CORE | Summary: Protein interaction with histone chaperone Reason: IPI documentation of chaperone interactions. Supporting Evidence: PMID:29300933 Structural characterization of the Asf1-Rtt109 interaction and its role in histone acetylation. |
| GO:0043992 histone H3K9 acetyltransferase activity | IDA PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications... | ACCEPT | Summary: Histone H3K9 acetyltransferase activity confirmed by direct assay Reason: Biochemical evidence demonstrates RTT109 catalyzes H3K9 acetylation on newly synthesized H3. Supporting Evidence: PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation. |
| GO:0043992 histone H3K9 acetyltransferase activity | IDA PMID:29300933 Structural characterization of the Asf1-Rtt109 interaction a... | ACCEPT | Summary: H3K9 acetyltransferase activity by Rtt109 Reason: Direct enzymatic assay confirms H3K9 as Rtt109 substrate. Supporting Evidence: PMID:29300933 Structural characterization of the Asf1-Rtt109 interaction and its role in histone acetylation. |
| GO:0070775 H3 histone acetyltransferase complex | IPI PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications... | ACCEPT | Summary: RTT109 is part of H3 histone acetyltransferase complex Reason: RTT109 associates with Vps75 and Asf1 histone chaperones to form active H3 acetyltransferase complexes. Supporting Evidence: PMID:21256037 Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation. file:yeast/RTT109/RTT109-deep-research-falcon.md Rtt109 forms functional HAT complexes with **Asf1** or **Vps75**; these are **functionally distinct**, with Asf1-linked activity being particularly important for genotoxic resistance |
| GO:0032931 histone H3K56 acetyltransferase activity | IDA PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by... | ACCEPT | Summary: H3K56 acetyltransferase activity IDA evidence Reason: Direct biochemical assay of H3K56 acetylation catalyzed by RTT109. Supporting Evidence: PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by Rtt109. |
| GO:0032931 histone H3K56 acetyltransferase activity | IMP PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by... | ACCEPT | Summary: H3K56 acetyltransferase activity IMP evidence Reason: Mutant phenotype: RTT109 mutants unable to acetylate H3K56. Supporting Evidence: PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by Rtt109. |
| GO:0061733 protein-lysine-acetyltransferase activity | IMP PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by... | ACCEPT | Summary: Protein-lysine-acetyltransferase activity demonstrated Reason: Enzymatic characterization confirms lysine acetylation from acetyl-CoA. Supporting Evidence: PMID:18707894 Structural insights into histone H3 lysine 56 acetylation by Rtt109. file:yeast/RTT109/RTT109-deep-research-falcon.md Rtt109 catalyzes **acetyl transfer from acetylβCoA to the Ξ΅βamine of lysine residues on histone H3**, producing acetylβlysine and CoA |
| GO:0005515 protein binding | IPI PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acet... | KEEP AS NON CORE | Summary: RTT109-Vps75 protein interaction Reason: Direct IPI evidence of physical association. Supporting Evidence: PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acetylation specificity. |
| GO:0032931 histone H3K56 acetyltransferase activity | IDA PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acet... | ACCEPT | Summary: Protein binding with histone chaperone NAP1 Reason: Documented interaction with NAP1. Supporting Evidence: PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acetylation specificity. |
| GO:0043992 histone H3K9 acetyltransferase activity | IDA PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acet... | ACCEPT | Summary: H3K56 acetyltransferase activity Reason: Additional direct evidence of this core enzymatic function. Supporting Evidence: PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acetylation specificity. |
| GO:0070775 H3 histone acetyltransferase complex | IDA PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acet... | ACCEPT | Summary: Histone H3K9 acetyltransferase activity Reason: Confirmation of H3K9 as RTT109 substrate. Supporting Evidence: PMID:31387991 Histone chaperone exploits intrinsic disorder to switch acetylation specificity. |
| GO:0032931 histone H3K56 acetyltransferase activity | IDA PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected str... | ACCEPT | Summary: RTT109 component of H3 histone acetyltransferase complex Reason: Direct observation of RTT109 in functional complex. Supporting Evidence: PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. |
| GO:0032931 histone H3K56 acetyltransferase activity | IMP PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected str... | ACCEPT | Summary: RTT109 protein interaction with Vps75 Reason: IPI documentation of robust interaction. Supporting Evidence: PMID:18568037 Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. |
| GO:0036408 histone H3K14 acetyltransferase activity | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: Part of H3 histone acetyltransferase complex Reason: RTT109 is integral component of Rtt109-Vps75-Asf1 acetyltransferase complex. Supporting Evidence: PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0043992 histone H3K9 acetyltransferase activity | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: Nuclear localization annotation Reason: Curated from homologous proteins and direct localization studies. Supporting Evidence: PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0043994 histone H3K23 acetyltransferase activity | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: Replication-born DSB repair via sister chromatid exchange Reason: RTT109 H3K56 acetylation promotes double-strand break repair by homologous recombination using sister chromatid. Essential function during replication-associated DNA damage. Supporting Evidence: PMID:23357952 Histone H3K56 acetylation controls the choice of DSB repair template PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0044017 histone H3K27 acetyltransferase activity | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: Regulation of double-strand break repair via nonhomologous end joining Reason: RTT109-Vps75 complex affects NHEJ pathway efficiency. Supporting Evidence: PMID:18036332 Interacting proteins Rtt109 and Vps75 affect the efficiency of non-homologous end-joining PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0032931 histone H3K56 acetyltransferase activity | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: NHEJ pathway regulation by RTT109 Reason: RTT109 controls double-strand break repair pathway choice. Supporting Evidence: PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0070775 H3 histone acetyltransferase complex | IDA PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H... | ACCEPT | Summary: Regulation of gene expression too broad Reason: Too general term. More specific transcription regulation annotations already present. RTT109 primary function is nucleosome assembly, secondary role is transcriptional regulation during S-phase. Supporting Evidence: PMID:31194870 Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. |
| GO:0005515 protein binding | IPI PMID:20560668 Kinetic mechanism of the Rtt109-Vps75 histone acetyltransfer... | KEEP AS NON CORE | Summary: Nuclear localization by direct observation Reason: Direct experimental evidence of RTT109 in nucleus. Supporting Evidence: PMID:20560668 Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. |
| GO:0070775 H3 histone acetyltransferase complex | IDA PMID:20560668 Kinetic mechanism of the Rtt109-Vps75 histone acetyltransfer... | ACCEPT | Summary: Histone H3 acetyltransferase activity Reason: Mutant phenotype confirms H3 acetylation function. Supporting Evidence: PMID:20560668 Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. |
| GO:0005634 nucleus | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: H3 acetyltransferase activity by direct assay Reason: Biochemical evidence of H3 acetylation. Supporting Evidence: PMID:14562095 Global analysis of protein localization in budding yeast. |
| GO:1990414 replication-born double-strand break repair via sister chromatid exchange | IMP PMID:23357952 Histone H3K56 acetylation, Rad52, and non-DNA repair factors... | ACCEPT | Summary: H3 acetyltransferase activity mutant evidence Reason: Genetic evidence confirms function. Supporting Evidence: PMID:23357952 Histone H3K56 acetylation, Rad52, and non-DNA repair factors control double-strand break repair choice with the sister chromatid. |
| GO:2001032 regulation of double-strand break repair via nonhomologous end joining | IMP PMID:18036332 Interacting proteins Rtt109 and Vps75 affect the efficiency ... | ACCEPT | Summary: H3 acetyltransferase activity Reason: Direct enzymatic assay. Supporting Evidence: PMID:18036332 Interacting proteins Rtt109 and Vps75 affect the efficiency of non-homologous end-joining in Saccharomyces cerevisiae. |
| GO:2001032 regulation of double-strand break repair via nonhomologous end joining | IMP PMID:27222517 Asf1 facilitates dephosphorylation of Rad53 after DNA double... | ACCEPT | Summary: H3 acetyltransferase activity Reason: Mutant phenotype demonstrates function. Supporting Evidence: PMID:27222517 Asf1 facilitates dephosphorylation of Rad53 after DNA double-strand break repair. |
| GO:0010468 regulation of gene expression | IMP PMID:26941319 Expression homeostasis during DNA replication. | ACCEPT | Summary: H3 acetyltransferase activity Reason: Genetic interaction evidence. Supporting Evidence: PMID:26941319 Expression homeostasis during DNA replication. |
| GO:0005634 nucleus | IDA PMID:15282802 Localization of proteins that are coordinately expressed wit... | ACCEPT | Summary: Histone H3K14 acetyltransferase activity Reason: RTT109 acetylates H3K14 on newly synthesized histones. Essential for R-loop prevention and DNA damage response. Supporting Evidence: PMID:15282802 Localization of proteins that are coordinately expressed with Cln2 during the cell cycle. |
| GO:0010484 histone H3 acetyltransferase activity | IMP PMID:17046836 Rtt109 is required for proper H3K56 acetylation: a chromatin... | ACCEPT | Summary: H3K23 acetyltransferase activity by direct assay Reason: Biochemical confirmation of H3K23 as substrate. Supporting Evidence: PMID:17046836 Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. |
| GO:0010484 histone H3 acetyltransferase activity | IDA PMID:17272722 Yeast Rtt109 promotes genome stability by acetylating histon... | ACCEPT | Summary: Histone H3K27 acetyltransferase activity Reason: RTT109-Vps75 acetylates H3K27 on newly synthesized histones. Supporting Evidence: PMID:17272722 Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. |
| GO:0010484 histone H3 acetyltransferase activity | IMP PMID:17272722 Yeast Rtt109 promotes genome stability by acetylating histon... | ACCEPT | Summary: H3K56 acetyltransferase activity Reason: Additional direct evidence of core function. Supporting Evidence: PMID:17272722 Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. |
| GO:0010484 histone H3 acetyltransferase activity | IDA PMID:17272723 Rtt109 acetylates histone H3 lysine 56 and functions in DNA ... | ACCEPT | Summary: Part of H3 histone acetyltransferase complex Reason: RTT109 component of complex. Supporting Evidence: PMID:17272723 Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. |
| GO:0010484 histone H3 acetyltransferase activity | IMP PMID:17272723 Rtt109 acetylates histone H3 lysine 56 and functions in DNA ... | ACCEPT | Summary: Transposable element silencing through chromatin acetylation Reason: RTT109 promotes silencing of Ty1 transposable elements. Originally identified as Regulator of Ty1 transposition protein 109. H3K56 acetylation contributes to heterochromatin state at silenced loci. Supporting Evidence: PMID:11779788 Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance PMID:17272723 Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. |
| GO:0010484 histone H3 acetyltransferase activity | IMP PMID:18458063 Chaperone control of the activity and specificity of the his... | ACCEPT | Summary: Maintenance of ribosomal DNA silencing Reason: RTT109 prevents hyper-amplification of ribosomal RNA genes through histone modification. Supporting Evidence: PMID:23593017 Rtt109 prevents hyper-amplification of ribosomal RNA genes through histone modification PMID:18458063 Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. |
| GO:0010484 histone H3 acetyltransferase activity | IGI PMID:18458063 Chaperone control of the activity and specificity of the his... | ACCEPT | Summary: H3K9 acetyltransferase activity Reason: RTT109 catalyzes H3K9 acetylation. Supporting Evidence: PMID:18458063 Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. |
| GO:0010526 transposable element silencing | IMP PMID:11779788 Multiple regulators of Ty1 transposition in Saccharomyces ce... | ACCEPT | Summary: H3K23 acetyltransferase activity Reason: RTT109 catalyzes H3K23 acetylation. Supporting Evidence: PMID:11779788 Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. |
| GO:0043007 maintenance of rDNA | IGI PMID:23593017 Rtt109 prevents hyper-amplification of ribosomal RNA genes t... | ACCEPT | Summary: TODO: Review this GOA annotation Supporting Evidence: PMID:23593017 Rtt109 prevents hyper-amplification of ribosomal RNA genes through histone modification in budding yeast. |
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