DNMT3A is a conserved de novo DNA cytosine-5 methyltransferase associated with nuclear chromatin and gene-expression regulation. The selected horse model retains the ADD and catalytic domains but lacks a segment overlapping the end of the PWWP chromatin-reader domain, leaving its normal histone-guided genomic targeting uncertain. DNMT3A expression has been measured during horse testis development.
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0000122 negative regulation of transcription by RNA polymerase II
IEA GO_REF:0000107
ACCEPT
Summary: The retained DNMT3A catalytic machinery supports gene-expression regulation.
Reason: The ADD and methyltransferase domains are conserved, supporting targeted DNA methylation and transcriptional effects. A PWWP deletion can change genomic targeting without eliminating the broad regulatory function.
Summary: Normal heterochromatin targeting is uncertain for this PWWP-altered model.
Reason: The selected sequence lacks human339–374, overlapping the PWWP reader. Human PWWP variants alter histone recognition and genomic methylation, so exact chromatin targeting cannot be inferred from an intact catalytic domain.
Summary: Normal heterochromatin targeting is uncertain for this PWWP-altered model.
Reason: The selected sequence lacks human339–374, overlapping the PWWP reader. Human PWWP variants alter histone recognition and genomic methylation, so exact chromatin targeting cannot be inferred from an intact catalytic domain.
The ADD domain (human 482–614) and C-terminal methyltransferase domain (634–912) are retained.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
IEA GO_REF:0000107
UNDECIDED
Summary: The proposed cis-regulatory sequence specificity needs independent support.
Reason: DNMT3A binds substrate DNA, but regulatory-site occupancy can be mediated by transcription factors. Neither the broad catalytic function nor the altered horse chromatin-reader region establishes this specific transcription-factor-like DNA-binding term.
Summary: This specialized recruitment or germline function needs target-specific transfer evidence.
Reason: Conserved methyltransferase activity is insufficient to establish a particular lncRNA/transcription-factor partner or specialized germ-cell pathway. The PWWP deletion adds uncertainty about normal genomic recruitment; the horse testis expression study is not a functional perturbation.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Summary: The conserved DNMT3A catalytic apparatus supports DNA recognition and methyltransferase-complex function.
Reason: The ADD and C-terminal catalytic domains remain in a near-identical horse sequence, matching primary biochemical/structural evidence for the family. The PWWP lesion concerns targeting and does not itself remove this catalytic apparatus.
The ADD domain (human 482–614) and C-terminal methyltransferase domain (634–912) are retained.
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
IBA GO_REF:0000033
ACCEPT
Summary: The conserved DNMT3A catalytic apparatus supports DNA recognition and methyltransferase-complex function.
Reason: The ADD and C-terminal catalytic domains remain in a near-identical horse sequence, matching primary biochemical/structural evidence for the family. The PWWP lesion concerns targeting and does not itself remove this catalytic apparatus.
The ADD domain (human 482–614) and C-terminal methyltransferase domain (634–912) are retained.
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
IEA GO_REF:0000120
ACCEPT
Summary: The conserved DNMT3A catalytic apparatus supports DNA recognition and methyltransferase-complex function.
Reason: The ADD and C-terminal catalytic domains remain in a near-identical horse sequence, matching primary biochemical/structural evidence for the family. The PWWP lesion concerns targeting and does not itself remove this catalytic apparatus.
Reason: Human imaging and conserved chromatin/catalytic machinery support nuclear/nucleoplasmic localization. Horse testis immunofluorescence demonstrates a DNMT3A protein pool but the cached abstract does not provide the detailed subcellular distribution or establish identity with this exact model.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Reason: Human imaging and conserved chromatin/catalytic machinery support nuclear/nucleoplasmic localization. Horse testis immunofluorescence demonstrates a DNMT3A protein pool but the cached abstract does not provide the detailed subcellular distribution or establish identity with this exact model.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Reason: Human imaging and conserved chromatin/catalytic machinery support nuclear/nucleoplasmic localization. Horse testis immunofluorescence demonstrates a DNMT3A protein pool but the cached abstract does not provide the detailed subcellular distribution or establish identity with this exact model.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Summary: A cytoplasmic DNMT3A pool is compatible with mammalian localization.
Reason: Retain the additional ortholog/phylogenetic localization. It is not the principal compartment for DNA methylation, and the horse expression study does not determine its biochemical role.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Summary: A cytoplasmic DNMT3A pool is compatible with mammalian localization.
Reason: Retain the additional ortholog/phylogenetic localization. It is not the principal compartment for DNA methylation, and the horse expression study does not determine its biochemical role.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
GO:0006346 DNA methylation-dependent constitutive heterochromatin formation
IEA GO_REF:0000107
UNDECIDED
Summary: Normal heterochromatin targeting is uncertain for this PWWP-altered model.
Reason: The selected sequence lacks human339–374, overlapping the PWWP reader. Human PWWP variants alter histone recognition and genomic methylation, so exact chromatin targeting cannot be inferred from an intact catalytic domain.
Summary: The retained DNMT3A catalytic machinery supports gene-expression regulation.
Reason: The ADD and methyltransferase domains are conserved, supporting targeted DNA methylation and transcriptional effects. A PWWP deletion can change genomic targeting without eliminating the broad regulatory function.
Summary: This specialized recruitment or germline function needs target-specific transfer evidence.
Reason: Conserved methyltransferase activity is insufficient to establish a particular lncRNA/transcription-factor partner or specialized germ-cell pathway. The PWWP deletion adds uncertainty about normal genomic recruitment; the horse testis expression study is not a functional perturbation.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
The ADD domain (human 482–614) and C-terminal methyltransferase domain (634–912) are retained.
GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation
IEA GO_REF:0000107
ACCEPT
Summary: The retained DNMT3A catalytic machinery supports gene-expression regulation.
Reason: The ADD and methyltransferase domains are conserved, supporting targeted DNA methylation and transcriptional effects. A PWWP deletion can change genomic targeting without eliminating the broad regulatory function.
Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells.
GO:0045892 negative regulation of DNA-templated transcription
IBA GO_REF:0000033
ACCEPT
Summary: The retained DNMT3A catalytic machinery supports gene-expression regulation.
Reason: The ADD and methyltransferase domains are conserved, supporting targeted DNA methylation and transcriptional effects. A PWWP deletion can change genomic targeting without eliminating the broad regulatory function.
Summary: This specialized recruitment or germline function needs target-specific transfer evidence.
Reason: Conserved methyltransferase activity is insufficient to establish a particular lncRNA/transcription-factor partner or specialized germ-cell pathway. The PWWP deletion adds uncertainty about normal genomic recruitment; the horse testis expression study is not a functional perturbation.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Summary: This specialized recruitment or germline function needs target-specific transfer evidence.
Reason: Conserved methyltransferase activity is insufficient to establish a particular lncRNA/transcription-factor partner or specialized germ-cell pathway. The PWWP deletion adds uncertainty about normal genomic recruitment; the horse testis expression study is not a functional perturbation.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Summary: Cysteine automethylation is a plausible conserved side reaction.
Reason: Mouse Dnmt3a exhibits slow catalytic-cysteine automethylation in DNA-free assays. Conservation of the catalytic region makes this capacity plausible, but neither horse evidence nor the source paper establishes a physiological protein-methylation role.
In the presence of CpG containing dsDNA, which is the natural substrate for Dnmt3a, the transfer of the methyl group from AdoMet to the flipped target base was preferred and auto-methylation was not detected.
The ADD domain (human 482–614) and C-terminal methyltransferase domain (634–912) are retained.
GO:0141196 transposable element silencing by piRNA-mediated DNA methylation
IEA GO_REF:0000107
UNDECIDED
Summary: This specialized recruitment or germline function needs target-specific transfer evidence.
Reason: Conserved methyltransferase activity is insufficient to establish a particular lncRNA/transcription-factor partner or specialized germ-cell pathway. The PWWP deletion adds uncertainty about normal genomic recruitment; the horse testis expression study is not a functional perturbation.
Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development.
Summary: The conserved DNMT3A catalytic apparatus supports DNA recognition and methyltransferase-complex function.
Reason: The ADD and C-terminal catalytic domains remain in a near-identical horse sequence, matching primary biochemical/structural evidence for the family. The PWWP lesion concerns targeting and does not itself remove this catalytic apparatus.
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Gene-expression regulation follows from the conserved DNA methyltransferase mechanism and is already present in frozen horse GOA. The PWWP-region deletion can alter which loci are methylated without abolishing the broad function. This known-target classification denotes overlap with the frozen annotation snapshot, not verified presence in ProtNLM training data.
Supporting Evidence:
PMID:29414941: "the DNMT3A-DNMT3L-DNA complex in which two DNMT3A monomers simultaneously attack two cytosine-phosphate-guanine (CpG) dinucleotides"
PMID:23042785: "DNMT3A recruitment is increased, with hypermethylation being associated with silencing of gene expression."
PMID:30478443: "Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells."
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Human imaging directly establishes a nuclear DNMT3A pool, and the horse model retains the chromatin-associated ADD/catalytic apparatus. The frozen horse GOA contains the more specific nucleoplasm term, supported by this same biological rationale. Horse testis protein-expression evidence is relevant but does not identify this accession or resolve precise compartments in the cached abstract.
Supporting Evidence:
PMID:23042785: "co-expression of WT1 and DNMT3A proteins in nuclei of blastemal cells in human fetal kidney and Wilms' tumours."
PMID:12138111: "Unlike Dnmt3a, which was concentrated on heterochromatin, Dnmt3a2 displayed a localization pattern suggestive of euchromatin association."
PMID:38705424: "Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development."