DNMT3L (DNA methyltransferase 3-like) is a catalytically inactive member of the DNMT3 family that regulates de novo DNA methylation. It has an amino-terminal ADD (ATRX-DNMT3-DNMT3L) cysteine-rich zinc-binding domain, which binds the amino-terminal tail of histone H3 when lysine 4 is unmethylated, and a carboxy-terminal methyltransferase-like domain that lacks the catalytic motifs of active DNA methyltransferases. Through the carboxy-terminal domain DNMT3L binds the catalytic domains of DNMT3A and DNMT3B, forming heterotetramers in which DNMT3L stimulates DNA and S-adenosyl-L-methionine binding and methyl transfer by its partner. DNMT3L is a nuclear protein expressed mainly in germ cells during the periods of de novo methylation and in embryonic stem cells. In mouse it is required to establish maternal methylation imprints in oocytes and to methylate and silence retrotransposons in prospermatogonia, where it acts with the piRNA pathway. In embryonic stem cells it also limits methylation at bivalent, Polycomb-marked promoters by competing with DNMT3A and DNMT3B for PRC2. The horse protein A0A9L0T837 is a full-length product of the DNMT3L gene in the same PANTHER subfamily as human and mouse DNMT3L; its function is inferred from those orthologs, since no horse-specific assay has been reported.
Summary: Ensembl Compara transfer of the mouse Dnmt3l heterochromatin localization (mouse IDA, PMID:11934864, co-localization with Dnmt3a/Dnmt3b in nuclei of transfected cells).
Reason: The source observation is co-localization of overexpressed Dnmt3L with Dnmt3a and Dnmt3b in transfected-cell nuclei (Hata et al. 2002). This is consistent with DNMT3L acting where de novo methylation takes place, but the localization was seen on overexpression, and DNMT3L function is defined by its partners and by H3K4me0 chromatin rather than by heterochromatin as such. Horse and mouse proteins are in the same PANTHER subfamily (PTHR23068:SF13), so the transfer is phylogenetically sound. The previous review accepted this as core; it is better kept as a non-core location.
Summary: Ensembl Compara transfer of a mouse Dnmt3l IDA localization (PMID:16543361) to condensed nuclear chromosome.
Reason: The mouse source annotation is an IDA from Xie et al. 2006, a paper on DNMT3B regulation by DNMT3L whose cached record is abstract-only, so the localization experiment cannot be inspected here. The curator read the full text; association of DNMT3L with chromosomes is consistent with its histone H3 tail binding and its partnership with chromatin-bound DNMT3A/3B. The transfer is within PANTHER SF13. The location is peripheral to the core regulatory activity, so it is kept as non-core.
The main proteins that interact in vivo with the product of an epitope-tagged allele of the endogenous Dnmt3L gene were identified by mass spectrometry as DNMT3A2, DNMT3B and the four core histones.
Summary: Nuclear localization inherited from the deep PTN001497036 node of the DNMT3/DRM family, which includes mouse Dnmt3l among its descendant evidences.
Reason: DNMT3L acts on chromatin, binding histone H3 tails and the DNMT3A/3B methyltransferases in the nucleus. The PAINT node is ancestral to all DNMT3 and plant DRM proteins, and mouse Dnmt3l (MGI:1859287) is one of the experimental donors. Horse DNMT3L sits in subfamily SF13 inside this clade and has no evidence of loss.
The main proteins that interact in vivo with the product of an epitope-tagged allele of the endogenous Dnmt3L gene were identified by mass spectrometry as DNMT3A2, DNMT3B and the four core histones.
Summary: Combined electronic annotation of nuclear localization, consistent with the IBA row and with experimental data for mouse and human DNMT3L.
Reason: Same claim as the nucleus IBA row; DNMT3L is a chromatin-associated nuclear regulator of de novo methylation, and the transfer is within PANTHER SF13.
Summary: Cytoplasmic pool inherited from the vertebrate DNMT3 node PTN002747444 (donors include mouse Dnmt3a, Dnmt3l and human DNMT3A).
Reason: Mouse Dnmt3l has a direct cytoplasm IDA (PMID:16543361) and is one of the donors at this node, so the IBA is grounded and horse DNMT3L is within the clade. No function of DNMT3L is known to be executed in the cytoplasm; the observation most likely reflects a soluble pool before nuclear import. Kept as non-core location.
Summary: Ensembl Compara transfer of mouse Dnmt3l cytoplasm IDA (PMID:16543361).
Reason: Same claim as the cytoplasm IBA row; kept as non-core for consistency. The location is real for mouse Dnmt3l but has no known functional role.
GO:0006346 DNA methylation-dependent constitutive heterochromatin formation
IEA GO_REF:0000107
MODIFY
Summary: Correct but general; the specific DNMT3L-dependent heterochromatin process is piRNA-directed transposon methylation (GO:0141196), a descendant of this term that the gene already carries.
Reason: DNMT3L participates in DNA methylation-dependent silencing as the activating subunit of DNMT3A (and DNMT3C in rodents). Its best-documented heterochromatin-forming role is de novo methylation of dispersed retrotransposons in prospermatogonia. Tandem pericentric repeats, the classical constitutive heterochromatin, are methylated normally in Dnmt3l-null germ cells (Bourc'his and Bestor 2004), so the general term over-reaches unless restricted to the transposon case. GO:0141196 transposable element silencing by piRNA-mediated DNA methylation is an is_a descendant of GO:0006346 (verified via OLS hierarchy) and is already annotated to this gene.
Summary: Projection of a mouse knockout phenotype (meiotic failure in spermatocytes) that the source paper attributes to an earlier defect in cells that do express Dnmt3L.
Reason: The mouse IMP (Bourc'his and Bestor 2004) shows that Dnmt3l-null males have meiotic catastrophe, but the same paper states that spermatocytes do not express Dnmt3L. The meiotic failure is a downstream consequence of retrotransposon hypomethylation in perinatal prospermatogonia, not participation of DNMT3L in meiosis I. The GO term asserts that the gene product does some of the work of meiosis, which DNMT3L cannot do in cells where it is absent. Its real contribution is captured by the transposon-silencing and imprinting terms.
Summary: DNMT3L activates DNMT3A and DNMT3B; this IBA is placed at the DNMT3L-specific node PTN001891074 with mouse and human DNMT3L as donors.
Reason: Core molecular function. DNMT3L binds the catalytic domains of DNMT3A and DNMT3B through its C-terminal domain and stimulates their methyltransferase activity about 15-fold by accelerating DNA and AdoMet binding. The crystal structure of the DNMT3A-DNMT3L C-terminal domains shows DNMT3L supplying activating interfaces, not active sites. The PAINT curator placed this function at the DNMT3L node only, a deliberate restriction to the SF13 branch that includes horse A0A9L0T837. Human F261, required for DNMT3A binding, is conserved in horse (F301). No more specific GO term for DNA methyltransferase activator activity exists.
We show here that Dnmt3L stimulates the catalytic activity of the Dnmt3A and Dnmt3B enzymes by directly binding to their respective catalytic domains via its own C-terminal domain.
the carboxy-terminal domain of human Dnmt3L interacts with the catalytic domain of Dnmt3a, demonstrating that Dnmt3L has dual functions of binding the unmethylated histone tail and activating DNA methyltransferase.
Summary: Transfer of human DNMT3L binding to HDAC1 (IPI, PMID:12202768); DNMT3L also binds DNMT3A and DNMT3B.
Reason: Binding to enzymes (DNMT3A, DNMT3B, HDAC1) is real, but the informative function of the DNMT3A/3B interaction is already captured by enzyme activator activity. The HDAC1 interaction comes from overexpression and Gal4-tethering assays and its physiological role is not established. Kept as non-core.
Summary: Transfer of the mouse Dnmt3l IDA (PMID:24074865) showing association with PRC2 in embryonic stem cells.
Reason: Neri et al. 2013 showed that Dnmt3L interacts with PRC2 in mouse ESCs in competition with Dnmt3a and Dnmt3b; the colocalizes_with qualifier correctly says DNMT3L is not a subunit. The observation comes from one study in one cell type and has not been examined in germ cells, so it is kept as non-core. The previous UNDECIDED is resolved now that the source experiment has been traced.
We demonstrate that Dnmt3L interacts with the Polycomb PRC2 complex in competition with the DNA methyltransferases Dnmt3a and Dnmt3b to maintain low methylation levels at the H3K27me3 regions.
GO:0045814 negative regulation of gene expression, epigenetic
IEA GO_REF:0000107
ACCEPT
Summary: Epigenetic repression through DNMT3L-dependent de novo DNA methylation of imprinted loci and retrotransposons.
Reason: The source is a human IDA based on HDAC1-dependent repression (Deplus et al. 2002), which is a tethering assay. The term is nonetheless well supported by the core genetic findings that DNMT3L-dependent methylation silences the paternal allele at maternally imprinted genes and silences retrotransposons. It is an umbrella for both of these specific outcomes; only the transposon case has a more specific descendant term, so the umbrella is kept.
Lack of maternal methylation imprints in heterozygous embryos derived from homozygous mutant oocytes caused biallelic expression of genes that are normally expressed only from the allele of paternal origin.
Deletion of the Dnmt3L gene prevented the de novo methylation of both long-terminal-repeat (LTR) and non-LTR retrotransposons, which were transcribed at high levels in spermatogonia and spermatocytes.
We find that Dnmt3L can repress transcription and that this repression is dependent on HDAC1 and is relieved by treatment with the HDAC inhibitor trichostatin A.
GO:0045892 negative regulation of DNA-templated transcription
IBA GO_REF:0000033
KEEP AS NON CORE
Summary: Inherited from the vertebrate DNMT3 node PTN002747444, seeded by human DNMT3A.
Reason: DNMT3L represses transcription when tethered to a promoter (Deplus et al. 2002), and its methylation-dependent silencing of imprinted alleles and transposons decreases their transcription. Horse DNMT3L is a descendant of the node and nothing indicates loss of this property. The repression is indirect, through DNA methylation, and the epigenetic silencing terms describe it better, so this broad process is kept as non-core.
We find that Dnmt3L can repress transcription and that this repression is dependent on HDAC1 and is relieved by treatment with the HDAC inhibitor trichostatin A.
Summary: Projection of a mouse ESC knockdown phenotype (failed ESC-to-PGC differentiation, PMID:24074865).
Reason: In mouse ESCs, Dnmt3L knockdown impairs differentiation into primordial germ cell-like cells because the Rhox5 promoter becomes hypermethylated. DNMT3L's contribution is regulation of promoter methylation; the differentiation outcome is downstream of it. The finding comes from one in vitro differentiation system and is transferred electronically to horse. It is not wrong, but as a process annotation it overstates what DNMT3L does.
Summary: DNMT3L is required to establish maternal methylation imprints in oocytes, acting with DNMT3A.
Reason: Core process. Two independent knockout studies (Bourc'his et al. 2001; Hata et al. 2002) showed that oocytes lacking Dnmt3L fail to methylate maternally imprinted regions, causing biallelic expression and embryonic death. DNMT3L does part of the work of imprint establishment as the activating subunit of the DNMT3A de novo methyltransferase and as a reader of H3K4me0 chromatin. This is participation, not just necessity. The transfer to horse is within PANTHER SF13.
Bisulfite genomic sequencing of DNA from oocytes and embryos showed that removal of Dnmt3L prevented methylation of sequences that are normally maternally methylated.
Dnmt3L, a protein sharing homology with DNA methyltransferases, Dnmt3a and Dnmt3b, but lacking enzymatic activity, is essential for the establishment of maternal methylation imprints and appropriate expression of maternally imprinted genes.
GO:0090310 negative regulation of DNA methylation-dependent heterochromatin formation
IEA GO_REF:0000107
KEEP AS NON CORE
Summary: Transfer of the mouse ESC finding (IMP, PMID:24074865) that Dnmt3L limits DNA methylation at bivalent promoters.
Reason: Neri et al. 2013 found that Dnmt3L knockdown raises methylation at promoters of bivalent genes in mouse ESCs, which they explain by Dnmt3L competing with Dnmt3a/3b for PRC2. This context-specific negative regulatory role is opposite in sign to DNMT3L's dominant activating role. It has not yet been independently confirmed or tested in germ cells, so it is kept as non-core. The previous UNDECIDED is resolved now that the source experiment has been traced.
Thus, in ESCs, Dnmt3L counteracts the activity of de novo DNA methylases to maintain hypomethylation at promoters of bivalent developmental genes.
GO:0141196 transposable element silencing by piRNA-mediated DNA methylation
IEA GO_REF:0000107
ACCEPT
Summary: DNMT3L is part of the de novo methylation machinery that methylates retrotransposons in prospermatogonia downstream of the piRNA pathway.
Reason: Core process. Dnmt3l-null male germ cells fail to methylate LTR and non-LTR retrotransposons, which become highly expressed. DNMT3L, with DNMT3A, is the methylation machinery that the piRNA effector SPOCD1 associates with in fetal testis (mouse IPI source of this annotation). DNMT3L does part of the work of the process, as the activating subunit of the methyltransferase. The transfer is within PANTHER SF13. Horse retrotransposon methylation has not been tested directly.
Deletion of the Dnmt3L gene prevented the de novo methylation of both long-terminal-repeat (LTR) and non-LTR retrotransposons, which were transcribed at high levels in spermatogonia and spermatocytes.
Summary: Transferred from human DNMT3L structural IPIs (DNMT3A-DNMT3L and DNMT3B-DNMT3L complexes); correct but very general.
Reason: The complexes in question are the DNMT3A-DNMT3L and DNMT3B-DNMT3L heterotetramers, which have DNA methyltransferase activity (two catalytic DNMT3A/3B subunits flanked by DNMT3L). GO:0140020 DNA methyltransferase complex ("a protein complex that possesses DNA methyltransferase activity") is the specific term. DNMT3L contributes activating interfaces, not a catalytic site, which fits membership of a catalytic complex. Gowher et al. 2005 found the DNMT3A-DNMT3L interaction to be transient during catalysis, so the complex is dynamic.
The complexed C-terminal domains of Dnmt3a and Dnmt3L showed further dimerization through Dnmt3a-Dnmt3a interaction, forming a tetrameric complex with two active sites.
ISS PMID:17687327 DNMT3L connects unmethylated lysine 4 of histone H3 to de no...
NEW
Summary: The DNMT3L ADD domain binds the histone H3 N-terminal tail unmethylated at lysine 4, shown by peptide binding, co-crystal structure and binding-site mutagenesis of human/mouse DNMT3L.
Reason: This is an activity of DNMT3L itself (its ADD domain contacts the H3 tail directly), not a process it is needed for. It is one of the two activities that define DNMT3L, linking de novo methylation to chromatin lacking H3K4 methylation, and GOA has no histone-binding molecular function for DNMT3L in any species. The transfer to horse rests on membership of the same PANTHER subfamily (SF13) as the characterised human and mouse proteins, and on conservation of every ADD-domain cysteine (RESULTS-rereview.md). The specific H3-contact residues were not checked individually, so this is ISS, not a horse-specific claim.
Cocrystallization of DNMT3L with the tail of histone H3 revealed that the tail bound to the cysteine-rich domain of DNMT3L, and substitution of key residues in the binding site eliminated the H3 tail-DNMT3L interaction.
All cysteines in the human ADD domain (human 41-173) are conserved in horse
Core Functions
Activates the de novo DNA methyltransferases DNMT3A and DNMT3B by binding their catalytic domains through its catalytically inactive C-terminal methyltransferase-like domain, forming a DNA methyltransferase heterotetramer and accelerating DNA and AdoMet binding.
We show here that Dnmt3L stimulates the catalytic activity of the Dnmt3A and Dnmt3B enzymes by directly binding to their respective catalytic domains via its own C-terminal domain.
Human Phe261, whose substitution F261A abolishes binding to DNMT3A (UniProt Q9UJW3 MUTAGEN, PMID:17713477), aligns to horse Phe301.
Reads chromatin through its ADD domain, binding the histone H3 amino-terminal tail when lysine 4 is unmethylated, which links de novo DNA methylation to H3K4me0 chromatin.
DNMT3L specifically interacts with the extreme amino terminus of histone H3; this interaction was strongly inhibited by methylation at lysine 4 of histone H3 but was insensitive to modifications at other positions.
Q: Should GO have a DNA methyltransferase activator activity term (child of enzyme activator activity) so that DNMT3L's specific activating function is expressible?
Q: Is the meiotic catastrophe in Dnmt3l-null males fully explained by retrotransposon reactivation in prospermatogonia, given that spermatocytes do not express DNMT3L?
Q: Does horse DNMT3L, like mouse, function with a germline-specific DNMT3 paralog, or only with DNMT3A (DNMT3C is rodent-specific)?
Suggested Experiments
Experiment: Test whether recombinant horse DNMT3L C-terminal domain stimulates horse DNMT3A catalytic-domain methyltransferase activity and whether the F301A substitution abolishes binding and stimulation.
Experiment: Profile DNMT3L expression and retrotransposon/imprint methylation in equine fetal gonads and oocytes to confirm the germline timing seen in mouse.
External Prediction Reviews
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.
DNMT3L is a catalytically inactive nuclear regulator of DNMT3A/DNMT3B de novo DNA methylation. Both ProtNLM2 predictions are biologically correct for the conserved horse ortholog; nucleus is already carried by horse GOA, and regulation of gene expression is less precise than the horse annotation to negative regulation of gene expression, epigenetic.
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Mouse Dnmt3L co-localizes with Dnmt3a and Dnmt3b in nuclei, and DNMT3L acts on chromatin as the activating partner of these de novo methyltransferases. The horse sequence aligns across the full human protein with an N-terminal extension. Horse GOA already carries nucleus (IBA and IEA, both accepted in the gene review), so the prediction is correct but not novel.
Supporting Evidence:
PMID:11934864: "We also show that Dnmt3L interacts with Dnmt3a and Dnmt3b and co-localizes with these enzymes in the nuclei of transfected cells"
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Loss of mouse Dnmt3L abolishes maternal methylation imprints and causes biallelic expression of maternally imprinted genes, and human DNMT3L represses transcription in an HDAC1-dependent manner. The horse protein is a full-length ortholog. Horse GOA carries negative regulation of gene expression, epigenetic (GO:0045814), accepted in the gene review and an is_a descendant of GO:0010468, so this broad prediction is correct but less precise than the existing annotation.
Supporting Evidence:
PMID:11719692: "Lack of maternal methylation imprints in heterozygous embryos derived from homozygous mutant oocytes caused biallelic expression of genes that are normally expressed only from the allele of paternal origin."
PMID:12202768: "We find that Dnmt3L can repress transcription and that this repression is dependent on HDAC1 and is relieved by treatment with the HDAC inhibitor trichostatin A."
The downloaded human Q9UJW3 sequence (386 residues) and selected horse A0A9L0T837 sequence (426 residues) share 77.7% identity among 386 paired residues. Paired coverage is 100.0% of human and 90.6% of horse.
Full alignment, hashes, parameters and reproducible script: DNMT3L.json and compare.py.
Pairwise similarity supports homology but does not establish reciprocal orthology, intact gene models, conservation of targeting signals or every biological claim. Current UniProt sequences are compared; identity with the original ProtNLM input sequence is unverified.