id: MODULE:dna_cytosine_methylation_cycle title: DNA cytosine methylation cycle — de novo CpG methylation, UHRF1/DNMT1 maintenance, TET/TDG active demethylation and methyl-CpG readers; DNMT3A/DNMT3B/DNMT3L/UHRF1/DNMT1/TET1-3/TDG/MBD1/MBD2/MECP2/ZBTB33/ZBTB4/ZBTB38/ZFP57 description: >- In mammalian genomes most CpG dinucleotides carry 5-methylcytosine (5mC), whereas CpG islands at promoters are usually unmethylated. Methylation patterns are written, copied, erased and read by distinct sets of proteins that use the same nucleotide as their substrate. De novo methylation, which establishes patterns in the germline and the early embryo, is carried out by DNMT3A and DNMT3B. These transfer a methyl group from S-adenosyl-L-methionine to C5 of cytosine in unmethylated DNA. DNMT3L, which has no catalytic activity, binds the DNMT3A catalytic domain, stimulates it, and reads histone H3 tails unmethylated at lysine 4; it is needed to set up maternal imprints. After replication, CpGs are hemimethylated, carrying 5mC only on the parental strand. Maintenance methylation copies the pattern onto the daughter strand. UHRF1 binds hemimethylated CpG through its SRA domain and H3K9me3-marked chromatin through its tandem Tudor domain. Its RING domain then mono-ubiquitinates histone H3 at lysines 18 and 23. The replication foci targeting sequence of DNMT1 binds this dual-ubiquitin mark, which recruits DNMT1, relieves its autoinhibition and lets it methylate the daughter-strand cytosine. Active demethylation begins with the TET dioxygenases (TET1, TET2, TET3). These Fe(II)- and 2-oxoglutarate-dependent enzymes oxidise 5mC in turn to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Thymine DNA glycosylase (TDG) excises 5fC and 5caC, but not 5mC or 5hmC, and base excision repair then restores unmodified cytosine. Methylation also passes without repair, because 5hmC is not a substrate for DNMT1 maintenance. Methylated CpG is read by two structural families of proteins, separate from the SRA reader UHRF1. The methyl-CpG-binding-domain proteins are MBD1, MBD2 and MeCP2. The C2H2 zinc-finger proteins are Kaiso (ZBTB33), ZBTB4, ZBTB38 and the KRAB zinc-finger protein ZFP57. These readers recruit corepressor, histone deacetylase and histone methyltransferase complexes to methylated loci, and ZFP57 protects the methylation of imprinting control regions in the early embryo. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0001340 title: DNA modification pathway statement: >- The module boundary follows the RGD Pathway Ontology term and its interactive diagram. The diagram draws cytosine converted to 5-methylcytosine with S-adenosylmethionine as methyl donor (gene nodes Dnmt1, Dnmt3a and Dnmt3b), 5mC converted to 5hmC and 5hmC converted to 5fC and 5caC by the "TET proteins" node, 5mC, 5hmC and 5caC associated with "MBP proteins" (methyl-binding proteins), and cytosine associated with "non-methylated CpG readers". It links out to the base excision repair, histone modification and chromatin remodeling subpathway diagrams. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0001340.yaml). - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0001340.yaml title: RGD PW:0001340 record text (project snapshot) statement: >- The RGD record text divides the methyltransferases into maintenance and de novo roles, the basis for the two writer parts of this module. supporting_text: DNMT1 is considered a maintenance methyltransferase and the other two mostly function as de novo methyltransferases - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0001340.yaml title: RGD PW:0001340 record text (project snapshot) statement: >- The RGD record text groups the methyl-binding proteins into three structural families, which is the basis for the reader part. UHRF1 is modelled in the maintenance part and UHRF2 is left out (see notes). supporting_text: Of these, MBD1, 2 and 4 and MeCP2 are members of MBD family, Zbtb33 known as Kaiso, Zbtb4, Zbtb38 and Zfp57 are members of the zinc family and Uhrf1 and 2 are members of SRA family. - source_id: GO:0006304 title: DNA modification statement: >- The GO mapping recorded for PW:0001340 in the project's module seeds (skos:closeMatch). It is the module concept. GO has no current process term for cytosine methylation as such: GO:0006306 DNA methylation and its children are obsolete because they describe a molecular function. The writing steps are therefore grounded on their molecular functions, and the copying and erasing steps on GO:0141119 and GO:0141167. - source_id: PMID:10555141 title: DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. statement: DNMT3A and DNMT3B are the de novo methyltransferases. supporting_text: Our results indicate that both Dnmt3a and Dnmt3b function as de novo methyltransferases that play important roles in normal development and disease. - source_id: PMID:21817016 title: Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. statement: >- TET oxidation followed by TDG excision is the active demethylation route modelled here. supporting_text: These data suggest that oxidation of 5mC by Tet proteins followed by TDG-mediated base excision of 5caC constitutes a pathway for active DNA demethylation. - source_id: PMID:10499592 title: The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. statement: >- MBD4 is a CpG mismatch glycosylase that repairs deaminated 5mC; this is why it is left to the base excision repair subpathway rather than modelled as a reader or a demethylase (see notes). supporting_text: Here we show that MBD4, an unrelated mammalian protein that contains a methyl-CpG binding domain, can also efficiently remove thymine or uracil from a mismatches CpG site in vitro. - source_id: PMID:21817016 title: Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. statement: MBD4 does not excise 5caC, so it is not the demethylation glycosylase. supporting_text: MBD4, another DNA glycosylase that removes U or T opposite to G in the CpG sequence context (14), exhibited no activity toward 5caC. notes: >- Derived from the RGD Pathway Ontology diagram PW:0001340 (DNA modification pathway) through the RGD_PATHWAY_ONTOLOGY project's diagram->module route; GO mapping GO:0006304 DNA modification (closeMatch). RGD curates 28 human genes to PW:0001340, but the diagram draws only Dnmt1, Dnmt3a and Dnmt3b as gene nodes. The other members sit behind four group nodes ("TET proteins", "TET interacting partners", "MBP proteins", "non-methylated CpG readers"). The module models the 5-methylcytosine cycle as four parts: de novo methylation, maintenance methylation, active demethylation and methyl-CpG reading. Fourteen of the 28 RGD genes are modelled (DNMT1, DNMT3A, DNMT3B, TET1, TET2, TET3, UHRF1, MBD1, MBD2, MECP2, ZBTB33, ZBTB4, ZBTB38, ZFP57). Two genes not on the RGD list are added: DNMT3L and TDG. Boundary decisions follow. (1) De novo methylation is a part whose catalytic step is a variant set of DNMT3A and DNMT3B (ONE_OR_MORE, as the two enzymes overlap but differ in targets, e.g. DNMT3B for centromeric minor satellites). DNMT3L is added as an optional stimulatory annoton with enzyme activator activity GO:0008047. This matches its IDA annotation and the core function in the DNMT3L gene review. DNMT3L is needed for maternal imprints but is restricted to germ cells and the early embryo, which is why it is optional. DNMT3C, the rodent-specific de novo enzyme for young retrotransposons, has no human orthologue. It is not modelled here; modules/pirna_mediated_germline_silencing.yaml covers piRNA-directed methylation and names DNMT3C and DNMT3L in that setting. (2) Maintenance methylation follows the human GO-CAM gomodel:6882d2b800000042, the project's best-overlap model. UHRF1 reads hemimethylated DNA and H3K9me2/3 and ubiquitinates H3K18/H3K23. DNMT1 reads H3K18ub/H3K23ub, and that reading positively regulates its methyltransferase activity. Each activity is linked to its GO-CAM activity. The DNMT1 methyltransferase is grounded on GO:0051718 (acting on CpG substrates), the core function in the DNMT1 gene review. That term is a child of the GO-CAM's GO:0003886. The GO-CAM also models SMARCA3/HLTF (Q14527) as a second H3K23 ubiquitin ligase and H3K9me2/3 reader feeding DNMT1. HLTF is not on the RGD list and is not modelled here. Its evidence (PMID:40680746) shows H3K23 ubiquitination and H3K9me3 maintenance in colorectal cancer cells. That paper raises a role in DNMT1 recruitment only in its discussion, as a possibility, so this is recorded as a knowledge gap. The GO-CAM's part_of GO:0141119 assertion for the HLTF activities may need upstream review. Three further human GO-CAMs model the regulation of UHRF1 stability and H3K9me3 binding: PKA phosphorylation (gomodel:6882d2b800000403), USP7 deubiquitination (gomodel:6882d2b800000491) and CDK1 phosphorylation (gomodel:6882d2b800000559). They reuse the same UHRF1 and DNMT1 activities. They are regulation of the maintenance part and are linked only as secondary associations. USP7, PKA and CDK1 are not modelled. (3) Active demethylation is a two-step chain. The first step is TET oxidation, a variant set of TET1, TET2 and TET3 (ONE_OR_MORE). Each TET carries GO:0070579 DNA 5-methylcytosine dioxygenase activity, which is IDA or EXP for all three. The three Rhea reactions are RHEA:52636 (5mC to 5hmC), RHEA:53828 (5hmC to 5fC) and RHEA:53832 (5fC to 5caC). TDG excision is the second step. TDG is not on the RGD list, but RGD's text says that 5fC/5caC "may be substrates for glycosylases and subsequent targeting by the base excision repair (BER) pathway". TDG is that glycosylase (PMID:21817016, PMID:21862836), and the GO definition of GO:0141167 names it. TDG is therefore added, with GO:0019104 DNA N-glycosylase activity (IDA, IMP). GO has no 5fC- or 5caC-specific glycosylase term; this is an ontology gap, recorded here and not as a knowledge gap. Comparator check (human GOA only; mouse and rat were not checked): GO:0141167 is carried only by TDG (TAS). The TETs carry the sibling regulatory term GO:0044029 (TET1 and TET2 IDA), not GO:0141167. Because the GO:0141167 definition begins with "the enzymatic oxidation of the 5-methylcytosine", and the TETs perform that step, GO:0141167 is placed on the TET annotons. The missing TET GO:0141167 annotations are a curation gap and are not recorded as a knowledge gap. The downstream BER steps (AP site incision by APEX1, gap filling by POLB, ligation) belong to the RGD base excision repair subpathway PW:0000129. No base excision repair module exists in modules/ yet, so they are described but not modelled. Modelling them here would turn a general repair pathway into a part of this module. (4) MBD4 is on the RGD list as an MBD-family methyl-binding protein but is not modelled. It is a mismatch-specific glycosylase that removes T or U from G·T/G·U mispairs at CpG, the product of 5mC deamination (PMID:10499592). It has no activity on 5caC (PMID:21817016). Its role is to repair the mutagenic deamination of 5mC, which belongs to the BER subpathway, not the methylation cycle. Its methyl-CpG binding serves that repair role, not chromatin silencing. GO:0141169 (direct 5-methylcytosine excision) is the plant DME/ROS1 route, and MBD4 is not modelled there either. (5) Methyl-CpG reading is a part whose variant set is the two reader families (ONE_OR_MORE), each with its own nested variant set of proteins. MBD family members are MBD1 and MBD2 (GO:0008327 methyl-CpG binding, IDA) and MECP2 (GO:0010385 double-stranded methylated DNA binding, IMP; MECP2 has no experimental GO:0008327). MBD3, which does not bind methylated DNA (PMID:9774669), is not on the RGD list and is excluded. The zinc-finger family members are ZBTB33/Kaiso, ZBTB4 and ZBTB38 (each GO:0008327, IDA) and ZFP57. ZFP57 is kept as a reader because it binds the methylated TGCCGC hexanucleotide in imprinting control regions and recruits KAP1/TRIM28, DNMTs and UHRF1 to protect that methylation (PMID:22055183). Its function is grounded on GO:0010385, which is IDA for mouse Zfp57 in QuickGO (checked 2026-10-26). Human ZFP57 has only GO:0003682 chromatin binding as experimental support. UHRF2 shares the SRA domain but is not modelled. Its experimental annotations are ubiquitin and SUMO ligase activities, and none of the cited literature shows that it substitutes for UHRF1 in recruiting DNMT1. The readers' downstream effectors (SIN3A and histone deacetylase complexes for MeCP2 and MBD2, SETDB1 for MBD1, KAP1/TRIM28 for ZFP57) belong to the histone modification subpathway PW:0001338 and are not modelled; SIN3A is on the RGD list for this reason. (6) Out of scope. Five transcription factors are context or targets, not participants in the cycle: EBF1, SPI1/PU.1, NANOG, PPARG and PRDM14. They regulate, or are regulated by, methylation at specific loci (TET or DNMT recruitment, pluripotency and germline demethylation programmes), and none of them writes, erases or reads 5mC. The CXXC-domain unmethylated-CpG readers (CXXC1/CFP1, KDM2A, KDM2B; also the CXXC domains of KMT2A, MBD1 and TET1) form RGD's "non-methylated CpG readers" node. They are not a part here. Their reading of unmethylated CpG (GO:0045322 unmethylated CpG binding) recruits histone H3K4 methylation by SET1/COMPASS (CXXC1, KMT2A, KMT2C) and H3K36 demethylation (KDM2A/B) to CpG islands. These are histone-modification outputs belonging to PW:0001338, and they do not act on 5mC. OGT (TET-interacting partner; O-GlcNAcylation of TET and of histones) and SIN3A (TET1 and MeCP2 corepressor partner) are regulators or effectors and are left out under the same rule. Applying CLAUDE.md's substrate-versus-participant test, none of these proteins catalyses a step of methylation, oxidation or excision. The chromatin remodeling subpathway PW:0001339 is also out of scope. S-adenosylmethionine supply by the methionine cycle is substrate supply and is out of scope. Molecular functions come from each protein's experimental GO annotations in QuickGO (checked 2026-10-26). Gene reviews exist for DNMT1, DNMT3A, DNMT3B and DNMT3L, and their core functions were used. The other members have no review yet. No GO-CAM in gocams/index.tsv covers the TETs, TDG or any methyl-CpG reader (checked 2026-10-26). PANTHER family ids and PTNs are deliberately not asserted. module: id: dna_cytosine_methylation_cycle label: DNA cytosine methylation cycle module_type: BIOLOGICAL_PROCESS description: >- Cytosine in CpG is methylated de novo by DNMT3A/DNMT3B, copied after replication by UHRF1-recruited DNMT1, oxidised by TET enzymes to 5hmC, 5fC and 5caC and restored by TDG excision and base excision repair. Methylated CpG is read by MBD-family and zinc-finger proteins. concepts: - preferred_term: DNA modification term: id: GO:0006304 label: DNA modification description: >- The GO term mapped to PW:0001340. It covers both adding and removing the methyl mark. Its methylation children are obsolete, so the steps are refined at the part level. context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens description: >- Members are grounded on the human proteins; the RGD diagram is drawn for rat and the cycle is conserved across mammals. cellular_components: - preferred_term: chromatin term: id: GO:0000785 label: chromatin description: All writers, erasers and readers act on chromosomal DNA in chromatin. parts: - order: 1 role: de novo cytosine methylation node: id: de_novo_methylation label: De novo CpG methylation by DNMT3A/DNMT3B with DNMT3L module_type: REACTION description: >- Establishes methylation on unmethylated DNA, mainly in germ cells and the early embryo. DNMT3A and DNMT3B transfer the methyl group of SAM to cytosine C5; DNMT3L stimulates DNMT3A and targets it to chromatin unmethylated at H3K4. parts: - order: 1 role: de novo methyltransferase node: id: dnmt3_catalysis label: DNMT3A or DNMT3B DNA (cytosine-5-)-methyltransferase module_type: REACTION variant_sets: - id: dnmt3_enzyme label: De novo methyltransferase axis: enzyme paralog / genomic target selection: ONE_OR_MORE notes: >- The two enzymes overlap but are not redundant; double knockout abolishes de novo methylation in ES cells and embryos. variants: - id: dnmt3a_variant label: DNMT3A module_type: REACTION annotons: - id: dnmt3a_methyltransferase label: DNMT3A DNA (cytosine-5-)-methyltransferase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNMT3A term: id: UniProtKB:Q9Y6K1 label: DNA (cytosine-5)-methyltransferase 3A function: preferred_term: DNA (cytosine-5-)-methyltransferase activity term: id: GO:0003886 label: DNA (cytosine-5-)-methyltransferase activity substrates: - preferred_term: 2'-deoxycytidine in DNA term: id: CHEBI:85452 label: 2'-deoxycytidine 5'-monophosphate(1-) residue - preferred_term: S-adenosyl-L-methionine term: id: CHEBI:59789 label: S-adenosyl-L-methionine zwitterion products: - preferred_term: 5-methyl-2'-deoxycytidine in DNA term: id: CHEBI:85454 label: 5-methyl dCMP(1-) residue - preferred_term: S-adenosyl-L-homocysteine term: id: CHEBI:57856 label: S-adenosyl-L-homocysteine zwitterion evidence: - source_id: RHEA:13681 statement: >- a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H+; the Rhea reaction in the reviewed DNMT3A, DNMT3B and DNMT1 UniProt entries. processes: - preferred_term: negative regulation of gene expression via chromosomal CpG island methylation term: id: GO:0044027 label: negative regulation of gene expression via chromosomal CpG island methylation - preferred_term: genomic imprinting term: id: GO:0071514 label: genomic imprinting locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Principal de novo enzyme for germline imprints and developmental methylation; its core function in the DNMT3A gene review. evidence: - source_id: PMID:10555141 statement: Dnmt3a and Dnmt3b knockout blocks de novo methylation. supporting_text: Inactivation of both genes by gene targeting blocks de novo methylation in ES cells and early embryos, but it has no effect on maintenance of imprinted methylation patterns. - id: dnmt3b_variant label: DNMT3B module_type: REACTION annotons: - id: dnmt3b_methyltransferase label: DNMT3B DNA (cytosine-5-)-methyltransferase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNMT3B term: id: UniProtKB:Q9UBC3 label: DNA (cytosine-5)-methyltransferase 3B function: preferred_term: DNA (cytosine-5-)-methyltransferase activity term: id: GO:0003886 label: DNA (cytosine-5-)-methyltransferase activity substrates: - preferred_term: 2'-deoxycytidine in DNA term: id: CHEBI:85452 label: 2'-deoxycytidine 5'-monophosphate(1-) residue - preferred_term: S-adenosyl-L-methionine term: id: CHEBI:59789 label: S-adenosyl-L-methionine zwitterion products: - preferred_term: 5-methyl-2'-deoxycytidine in DNA term: id: CHEBI:85454 label: 5-methyl dCMP(1-) residue - preferred_term: S-adenosyl-L-homocysteine term: id: CHEBI:57856 label: S-adenosyl-L-homocysteine zwitterion evidence: - source_id: RHEA:13681 statement: Same reaction as DNMT3A. locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Required for methylation of centromeric minor satellite repeats; mutated in ICF syndrome. Its core function in the DNMT3B gene review. No processes are given, unlike DNMT3A: DNMT3B's GOA has no CpG-island silencing or imprinting term, and imprints are established by DNMT3A with DNMT3L. evidence: - source_id: PMID:10555141 statement: DNMT3B has a specific, nonoverlapping target class. supporting_text: Dnmt3a and Dnmt3b also exhibit nonoverlapping functions in development, with Dnmt3b specifically required for methylation of centromeric minor satellite repeats. - order: 2 role: stimulation and chromatin targeting of DNMT3A by DNMT3L optional: true node: id: dnmt3l_stimulation label: DNMT3L stimulation of DNMT3A module_type: REGULATORY_STEP description: >- Catalytically inactive DNMT3L forms a heterotetramer with the DNMT3A catalytic domain, stimulating it, and reads unmethylated H3K4 through its PHD-like domain. Required for maternal imprint establishment in oocytes; optional because it is restricted to germ cells and early embryos. annotons: - id: dnmt3l_activator label: DNMT3L enzyme activator activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNMT3L term: id: UniProtKB:Q9UJW3 label: DNA (cytosine-5)-methyltransferase 3-like function: preferred_term: enzyme activator activity term: id: GO:0008047 label: enzyme activator activity processes: - preferred_term: genomic imprinting term: id: GO:0071514 label: genomic imprinting locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Activator and chromatin-targeting cofactor of DNMT3A (and DNMT3B); core function in the DNMT3L gene review. evidence: - source_id: PMID:17713477 statement: The DNMT3L C-terminal domain binds and activates the DNMT3A catalytic domain. supporting_text: Dnmt3L has dual functions of binding the unmethylated histone tail and activating DNA methyltransferase - source_id: PMID:11934864 statement: DNMT3L is required for maternal methylation imprints. supporting_text: Dnmt3L, a protein sharing homology with DNA methyltransferases, Dnmt3a and Dnmt3b, but lacking enzymatic activity, is essential for the establishment of maternal methylation imprints connections: - source: dnmt3l_stimulation target: dnmt3_catalysis connection_type: POSITIVELY_REGULATES description: DNMT3L stimulates DNMT3A catalysis. - order: 2 role: maintenance methylation after DNA replication node: id: maintenance_methylation label: UHRF1-directed DNMT1 maintenance methylation module_type: BIOLOGICAL_PROCESS description: >- UHRF1 recognises hemimethylated CpG and H3K9me3, ubiquitinates H3K18 and H3K23, and the ubiquitin marks recruit and activate DNMT1, which methylates the daughter-strand cytosine. concepts: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication context: cellular_components: - preferred_term: replication fork term: id: GO:0005657 label: replication fork description: >- UHRF1 acts at replication forks; the location used for the UHRF1 activities in gomodel:6882d2b800000042. gocam_associations: - model: gomodel:6882d2b800000042 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: >- Best-overlap GO-CAM for PW:0001340; its UHRF1 and DNMT1 activities are linked on the annotons below. Its SMARCA3/HLTF activities are not modelled (see notes). - model: gomodel:6882d2b800000403 title: Phosphorylation of UHRF1 by PKA decreased UHRF1 binding to H3K9me3 (Human). description: Regulation of the UHRF1 H3K9me3-reading step; same UHRF1/DNMT1 activities. - model: gomodel:6882d2b800000491 title: USP7 mediates deubiquitination of UHRF1, preventing autoubiquitination and degradation of UHRF1 (Human). description: Regulation of UHRF1 stability; same UHRF1/DNMT1 activities. - model: gomodel:6882d2b800000559 title: Phosphorylation of UHRF1 by CDK1 prevents UHRF1 deubiquitination by USP7, promoting autoubiquitination and degradation of UHRF1 (Human). description: Regulation of UHRF1 stability in mitosis; same UHRF1/DNMT1 activities. parts: - order: 1 role: recognition of hemimethylated CpG and H3K9me3 chromatin node: id: uhrf1_recognition label: UHRF1 SRA and tandem Tudor reading module_type: MOLECULAR_FUNCTION annotons: - id: uhrf1_hemimethylated_dna_binding label: UHRF1 hemi-methylated DNA binding (SRA domain) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: UHRF1 term: id: UniProtKB:Q96T88 label: E3 ubiquitin-protein ligase UHRF1 function: preferred_term: hemi-methylated DNA-binding term: id: GO:0044729 label: hemi-methylated DNA-binding processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication locations: - preferred_term: replication fork term: id: GO:0005657 label: replication fork role_description: Senses the hemimethylated CpG left by replication. gocam_associations: - model: gomodel:6882d2b800000042 activity: gomodel:6882d2b800000042/6882d2b800000043 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: UHRF1 GO:0044729, part of GO:0141119, at the replication fork. evidence: - source_id: PMID:17673620 statement: The UHRF1 SRA domain binds hemimethylated CG preferentially. supporting_text: the SRA (SET and RING associated) domain, that shows strong preferential binding to hemimethylated CG sites, the physiological substrate for DNMT1 - source_id: PMID:17994007 statement: Np95/UHRF1 is required in vivo for maintenance methylation and loads DNMT1. supporting_text: Np95 forms complexes with Dnmt1 and mediates the loading of Dnmt1 to replicating heterochromatic regions. - id: uhrf1_h3k9me3_reader label: UHRF1 histone H3K9me2/3 reader (tandem Tudor domain) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: UHRF1 term: id: UniProtKB:Q96T88 label: E3 ubiquitin-protein ligase UHRF1 function: preferred_term: histone H3K9me2/3 reader activity term: id: GO:0062072 label: histone H3K9me2/3 reader activity processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication role_description: >- Couples maintenance methylation to H3K9me3 heterochromatin; reading is cooperative with hemimethylated DNA binding. gocam_associations: - model: gomodel:6882d2b800000042 activity: gomodel:6882d2b800000042/6882d2b800000066 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: UHRF1 GO:0062072, positively regulating its H3K18 ubiquitin ligase activity. evidence: - source_id: PMID:21489993 statement: The UHRF1 tandem Tudor domain reads H3K4me0/K9me3. supporting_text: UHRF1 contains a tandem Tudor domain (TTD) that recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3) - order: 2 role: histone H3 ubiquitination by UHRF1 node: id: uhrf1_h3_ubiquitination label: UHRF1 RING ubiquitination of H3K18 and H3K23 module_type: REACTION annotons: - id: uhrf1_h3k23_ubiquitin_ligase label: UHRF1 histone H3K23 ubiquitin ligase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: UHRF1 term: id: UniProtKB:Q96T88 label: E3 ubiquitin-protein ligase UHRF1 function: preferred_term: histone H3K23 ubiquitin ligase activity term: id: GO:0140234 label: histone H3K23 ubiquitin ligase activity processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication role_description: Writes the H3K23ub mark that DNMT1 reads. evidence: - source_id: PMID:24013172 statement: UHRF1-dependent H3K23 ubiquitylation is required for maintenance methylation. supporting_text: Here we show that Uhrf1-dependent histone H3 ubiquitylation has a prerequisite role in the maintenance DNA methylation. - source_id: PMID:24013172 statement: A UHRF1 RING mutant fails to recruit DNMT1. supporting_text: The RING finger mutant of Uhrf1 fails to recruit Dnmt1 to DNA replication sites and maintain DNA methylation in mammalian cultured cells. - id: uhrf1_h3k18_ubiquitin_ligase label: UHRF1 histone H3K18 ubiquitin ligase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: UHRF1 term: id: UniProtKB:Q96T88 label: E3 ubiquitin-protein ligase UHRF1 function: preferred_term: histone H3K18 ubiquitin ligase activity term: id: GO:0140248 label: histone H3K18 ubiquitin ligase activity processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication role_description: >- Writes the H3K18ub half of the dual mark; allosterically activated by hemimethylated DNA. gocam_associations: - model: gomodel:6882d2b800000042 activity: gomodel:6882d2b800000042/6882d2b800000057 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: UHRF1 GO:0140248, providing input for the DNMT1 H3K18ub reader activity. evidence: - source_id: PMID:27595565 statement: Hemimethylated DNA activates UHRF1 ubiquitylation of several H3 tail lysines. supporting_text: HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. - order: 3 role: DNMT1 recruitment, activation and daughter-strand methylation node: id: dnmt1_maintenance label: DNMT1 reading of H3K18ub/H3K23ub and CpG methylation module_type: REACTION annotons: - id: dnmt1_h3k23ub_reader label: DNMT1 histone H3K23ub reader activity (RFTS) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNMT1 term: id: UniProtKB:P26358 label: DNA (cytosine-5)-methyltransferase 1 function: preferred_term: histone H3K23ub reader activity term: id: GO:0140257 label: histone H3K23ub reader activity processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication role_description: >- The RFTS binds the two-mono-ubiquitin H3 mark, recruiting DNMT1 and opening its active site. gocam_associations: - model: gomodel:6882d2b800000042 activity: gomodel:6882d2b800000042/6882d2b800000094 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: DNMT1 GO:0140257, directly positively regulating DNMT1 methyltransferase activity. evidence: - source_id: PMID:29053958 statement: DNMT1 uses two-mono-ubiquitylated H3 for recruitment and activation. supporting_text: We demonstrate here that Dnmt1 utilizes two-mono-ubiquitylated histone H3 as a unique ubiquitin mark for its recruitment to and activation at DNA methylation sites. - id: dnmt1_h3k18ub_reader label: DNMT1 histone H3K18ub reader activity (RFTS) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNMT1 term: id: UniProtKB:P26358 label: DNA (cytosine-5)-methyltransferase 1 function: preferred_term: histone H3K18ub reader activity term: id: GO:0140254 label: histone H3K18ub reader activity processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication role_description: Second ubiquitin-binding contact of the RFTS. gocam_associations: - model: gomodel:6882d2b800000042 activity: gomodel:6882d2b800000042/6882d2b800000086 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: DNMT1 GO:0140254, directly positively regulating DNMT1 methyltransferase activity. evidence: - source_id: PMID:29053958 statement: Binding of H3K18Ub/K23Ub stimulates DNMT1 catalysis. supporting_text: Actually, incubation of Dnmt1 with H3-K18Ub/23Ub increases its catalytic activity in vitro. - id: dnmt1_methyltransferase label: DNMT1 CpG maintenance methyltransferase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DNMT1 term: id: UniProtKB:P26358 label: DNA (cytosine-5)-methyltransferase 1 function: preferred_term: DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates term: id: GO:0051718 label: DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates substrates: - preferred_term: 2'-deoxycytidine in hemimethylated CpG term: id: CHEBI:85452 label: 2'-deoxycytidine 5'-monophosphate(1-) residue - preferred_term: S-adenosyl-L-methionine term: id: CHEBI:59789 label: S-adenosyl-L-methionine zwitterion products: - preferred_term: 5-methyl-2'-deoxycytidine in DNA term: id: CHEBI:85454 label: 5-methyl dCMP(1-) residue - preferred_term: S-adenosyl-L-homocysteine term: id: CHEBI:57856 label: S-adenosyl-L-homocysteine zwitterion evidence: - source_id: RHEA:13681 statement: Same reaction as DNMT3A, on the hemimethylated daughter strand. processes: - preferred_term: chromosomal DNA methylation maintenance following DNA replication term: id: GO:0141119 label: chromosomal DNA methylation maintenance following DNA replication locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Maintenance methyltransferase; GO:0051718 is the core function in the DNMT1 gene review and refines the GO-CAM's GO:0003886. gocam_associations: - model: gomodel:6882d2b800000042 activity: gomodel:6882d2b800000042/6882d2b800000110 title: UHRF1 and SMARCA3 mediate histone H3 ubiquitination (H3K18ub and H3K23ub), promoting DNMT1 recruitment at hemimethylated DNA (Human). description: DNMT1 GO:0003886, part of GO:0141119 in heterochromatin. evidence: - source_id: PMID:17994007 statement: DNMT1 methylates the new strand opposite parental 5mC in S phase. supporting_text: Dnmt1 is needed in S phase to methylate newly replicated CpGs occurring opposite methylated ones on the mother strand of the DNA, which is essential for the epigenetic inheritance of methylation patterns in the genome. connections: - source: uhrf1_recognition target: uhrf1_h3_ubiquitination connection_type: POSITIVELY_REGULATES description: >- Hemimethylated DNA and H3K9me3 binding activate UHRF1 E3 activity on the H3 tail (GO-CAM: directly positively regulates). - source: uhrf1_h3_ubiquitination target: dnmt1_maintenance connection_type: PROVIDES_INPUT_FOR description: >- H3K18ub/H3K23ub is the mark bound by the DNMT1 RFTS (GO-CAM: provides input for). - order: 3 role: active demethylation by oxidation and excision node: id: active_demethylation label: TET oxidation and TDG excision module_type: BIOLOGICAL_PROCESS description: >- TET dioxygenases oxidise 5mC iteratively to 5hmC, 5fC and 5caC; TDG excises 5fC and 5caC, and base excision repair (RGD subpathway PW:0000129, not modelled) restores unmodified cytosine. concepts: - preferred_term: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway term: id: GO:0141167 label: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway parts: - order: 1 role: iterative oxidation of 5-methylcytosine node: id: tet_oxidation label: TET 5-methylcytosine dioxygenase module_type: REACTION description: >- Fe(II)/2-oxoglutarate-dependent oxidation: 5mC to 5hmC (RHEA:52636), 5hmC to 5fC (RHEA:53828), 5fC to 5caC (RHEA:53832). variant_sets: - id: tet_enzyme label: TET paralog axis: enzyme paralog / cell type selection: ONE_OR_MORE notes: >- TET1 predominates in embryonic and germ cells, TET2 and TET3 are broadly expressed (TET3 in the zygote); all three have the same catalytic activity. variants: - id: tet1_variant label: TET1 module_type: REACTION annotons: - id: tet1_dioxygenase label: TET1 DNA 5-methylcytosine dioxygenase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TET1 term: id: UniProtKB:Q8NFU7 label: Methylcytosine dioxygenase TET1 function: &tet_function preferred_term: DNA 5-methylcytosine dioxygenase activity term: id: GO:0070579 label: DNA 5-methylcytosine dioxygenase activity substrates: - preferred_term: 5-methyl-2'-deoxycytidine in DNA term: id: CHEBI:85454 label: 5-methyl dCMP(1-) residue - preferred_term: 2-oxoglutarate term: id: CHEBI:16810 label: 2-oxoglutarate(2-) - preferred_term: O2 term: id: CHEBI:15379 label: dioxygen products: - preferred_term: 5-hydroxymethyl-2'-deoxycytidine in DNA term: id: CHEBI:136731 label: 5-hydroxymethyldeoxycytidine 5'-monophosphate(1-) residue - preferred_term: 5-formyl-2'-deoxycytidine in DNA term: id: CHEBI:137731 label: 5-formyl-dCMP(1-) residue - preferred_term: 5-carboxyl-2'-deoxycytidine in DNA term: id: CHEBI:137732 label: 5-carboxy-dCMP(2-) residue - preferred_term: succinate term: id: CHEBI:30031 label: succinate(2-) - preferred_term: CO2 term: id: CHEBI:16526 label: carbon dioxide evidence: - source_id: RHEA:52636 statement: 5mC in DNA + 2-oxoglutarate + O2 = 5hmC in DNA + succinate + CO2. - source_id: RHEA:53828 statement: 5hmC in DNA + 2-oxoglutarate + O2 = 5fC in DNA + succinate + CO2 + H2O. - source_id: RHEA:53832 statement: 5fC in DNA + 2-oxoglutarate + O2 = 5caC in DNA + succinate + CO2 + H+. processes: &tet_processes - preferred_term: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway term: id: GO:0141167 label: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway - preferred_term: positive regulation of gene expression via chromosomal CpG island demethylation term: id: GO:0044029 label: positive regulation of gene expression via chromosomal CpG island demethylation locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Founding TET; its N-terminal CXXC domain also binds unmethylated CpG. evidence: - source_id: PMID:19372391 statement: TET1 is a 2OG/Fe(II)-dependent 5mC hydroxylase. supporting_text: TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro. - source_id: PMID:21778364 statement: TET proteins further oxidise to 5fC and 5caC. supporting_text: Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity-dependent manner. - id: tet2_variant label: TET2 module_type: REACTION annotons: - id: tet2_dioxygenase label: TET2 DNA 5-methylcytosine dioxygenase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TET2 term: id: UniProtKB:Q6N021 label: Methylcytosine dioxygenase TET2 function: *tet_function processes: *tet_processes locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Broadly expressed TET; frequently mutated in myeloid malignancies. Lacks a CXXC domain. evidence: - source_id: PMID:21778364 statement: Purified TET2 generates 5hmC, 5fC and 5caC. supporting_text: During this period, Tet2 is able to convert more than 95% of the 5mC to 5hmC (~60%), 5fC (~30%), and 5caC (5%) - source_id: PMID:21817016 statement: Purified TET2 oxidises 5mC or 5hmC DNA substrates. supporting_text: TLC analysis revealed that spot X could be generated by incubating the 5mC or 5hmC substrate with the purified Tet2 protein - id: tet3_variant label: TET3 module_type: REACTION annotons: - id: tet3_dioxygenase label: TET3 DNA 5-methylcytosine dioxygenase activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TET3 term: id: UniProtKB:O43151 label: Methylcytosine dioxygenase TET3 function: *tet_function processes: *tet_processes locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Broadly expressed TET; generates 5caC weakly in vitro compared with TET1 and TET2. evidence: - source_id: PMID:21778364 statement: TET3 shares the activity-dependent oxidation products, with weak 5caC formation. supporting_text: Similarly, Tet2 and Tet3 also generated three enzymatic activity-dependent radioactive spots that were detected in Tet1-catalyzed reaction - order: 2 role: excision of 5fC and 5caC node: id: tdg_excision label: TDG excision of 5fC and 5caC module_type: REACTION description: >- TDG hydrolyses the N-glycosidic bond of 5fC and 5caC in CpG context, leaving an abasic site for base excision repair. It does not act on 5mC or 5hmC. annotons: - id: tdg_glycosylase label: TDG DNA N-glycosylase activity on 5fC/5caC participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TDG term: id: UniProtKB:Q13569 label: G/T mismatch-specific thymine DNA glycosylase function: preferred_term: DNA N-glycosylase activity term: id: GO:0019104 label: DNA N-glycosylase activity substrates: - preferred_term: 5-formyl-2'-deoxycytidine in DNA term: id: CHEBI:137731 label: 5-formyl-dCMP(1-) residue - preferred_term: 5-carboxyl-2'-deoxycytidine in DNA term: id: CHEBI:137732 label: 5-carboxy-dCMP(2-) residue processes: - preferred_term: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway term: id: GO:0141167 label: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway - preferred_term: base-excision repair, AP site formation term: id: GO:0006285 label: base-excision repair, AP site formation locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- The glycosylase named in the GO:0141167 definition; not on the RGD gene list but required by RGD's text (5fC/5caC as glycosylase and BER substrates). Also excises T and U from G·T/G·U mispairs. evidence: - source_id: PMID:21817016 statement: TDG specifically recognises and excises 5caC; TDG depletion accumulates 5caC. supporting_text: 5caC is specifically recognized and excised by thymine-DNA glycosylase (TDG). Depletion of TDG in mouse embyronic stem cells leads to accumulation of 5caC to a readily detectable level. - source_id: PMID:21862836 statement: TDG rapidly excises 5fC and also 5caC, but not 5hmC. supporting_text: We show here that TDG rapidly removes fC, with higher activity than for G·T mispairs, and has substantial caC excision activity, yet it cannot remove hmC. - source_id: PMID:21496894 statement: TET1-promoted demethylation requires base excision repair. supporting_text: promotes DNA demethylation in mammalian cells through a process that requires the base excision repair pathway connections: - source: tet_oxidation target: tdg_excision connection_type: PROVIDES_INPUT_FOR description: 5fC and 5caC made by TET are the TDG substrates. - order: 4 role: reading of methylated CpG node: id: methyl_cpg_reading label: Methyl-CpG readers (MBD and zinc-finger families) module_type: MOLECULAR_FUNCTION description: >- Proteins that bind methylated CpG and recruit corepressor, histone deacetylase and histone methyltransferase complexes. The SRA-family reader UHRF1 is modelled in the maintenance part. variant_sets: - id: reader_family label: Methyl-CpG reader structural family axis: DNA-binding domain family selection: ONE_OR_MORE notes: >- Most cells express several readers of both families; tissue distribution differs (MeCP2 is highest in neurons, ZBTB4 and ZBTB38 in brain). variants: - id: mbd_family_readers label: Methyl-CpG-binding-domain (MBD) proteins module_type: MOLECULAR_FUNCTION variant_sets: - id: mbd_reader label: MBD reader axis: paralog selection: ONE_OR_MORE variants: - id: mbd1_variant label: MBD1 module_type: MOLECULAR_FUNCTION annotons: - id: mbd1_methyl_cpg_binding label: MBD1 methyl-CpG binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MBD1 term: id: UniProtKB:Q9UIS9 label: Methyl-CpG-binding domain protein 1 function: preferred_term: methyl-CpG binding term: id: GO:0008327 label: methyl-CpG binding locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- MBD-family reader that represses methylated promoters; some isoforms carry CXXC domains. evidence: - source_id: PMID:9774669 statement: MeCP2 and MBD1 bind methylated DNA through the MBD and repress transcription. supporting_text: MeCP2 and MBD1 (formerly PCM1) are two known proteins that bind specifically to methylated DNA via a related amino acid motif and that can repress transcription. - id: mbd2_variant label: MBD2 module_type: MOLECULAR_FUNCTION annotons: - id: mbd2_methyl_cpg_binding label: MBD2 methyl-CpG binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MBD2 term: id: UniProtKB:Q9UBB5 label: Methyl-CpG-binding domain protein 2 function: preferred_term: methyl-CpG binding term: id: GO:0008327 label: methyl-CpG binding locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Methyl-CpG-binding subunit that targets the NuRD deacetylase/remodeling complex to methylated DNA. evidence: - source_id: PMID:9774669 statement: MBD2 binds methyl-CpG in vitro and in vivo. supporting_text: The data demonstrate that MBD2 and MBD4 bind specifically to methyl-CpG in vitro and in vivo - id: mecp2_variant label: MeCP2 module_type: MOLECULAR_FUNCTION annotons: - id: mecp2_methylated_dna_binding label: MeCP2 methylated DNA binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MECP2 term: id: UniProtKB:P51608 label: Methyl-CpG-binding protein 2 function: preferred_term: double-stranded methylated DNA binding term: id: GO:0010385 label: double-stranded methylated DNA binding locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Abundant neuronal reader that recruits the SIN3A/histone deacetylase corepressor; mutated in Rett syndrome. evidence: - source_id: PMID:9620804 statement: MeCP2 binds chromosomes methylation-dependently and recruits a SIN3A/HDAC corepressor. supporting_text: MeCP2 binds tightly to chromosomes in a methylation-dependent manner. - source_id: PMID:9620804 statement: The MeCP2 repression domain associates with an mSin3A/histone deacetylase corepressor complex. supporting_text: a region of MeCP2 that localizes with the TRD associates with a corepressor complex containing the transcriptional repressor mSin3A and histone deacetylases - id: zinc_finger_readers label: C2H2 zinc-finger methyl-CpG readers module_type: MOLECULAR_FUNCTION variant_sets: - id: zf_reader label: Zinc-finger reader axis: paralog / target sequence selection: ONE_OR_MORE variants: - id: zbtb33_variant label: Kaiso (ZBTB33) module_type: MOLECULAR_FUNCTION annotons: - id: zbtb33_methyl_cpg_binding label: Kaiso methyl-CpG binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ZBTB33 (Kaiso) term: id: UniProtKB:Q86T24 label: Transcriptional regulator Kaiso function: preferred_term: methyl-CpG binding term: id: GO:0008327 label: methyl-CpG binding role_description: >- Binds symmetrically methylated CGCG through three Kruppel-like zinc fingers. evidence: - source_id: PMID:16354688 statement: Kaiso binds methylated CGCG through its zinc fingers. supporting_text: Kaiso, a structurally unrelated protein, has also been shown to bind methylated CGCGs through its three Krüppel-like C2H2 zinc fingers. - id: zbtb4_variant label: ZBTB4 module_type: MOLECULAR_FUNCTION annotons: - id: zbtb4_methyl_cpg_binding label: ZBTB4 methyl-CpG binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ZBTB4 term: id: UniProtKB:Q9P1Z0 label: Zinc finger and BTB domain-containing protein 4 function: preferred_term: methyl-CpG binding term: id: GO:0008327 label: methyl-CpG binding role_description: Kaiso-like reader that can bind a single methylated CpG. evidence: - source_id: PMID:16354688 statement: ZBTB4 and ZBTB38 bind methylated DNA, including single methyl-CpGs. supporting_text: We report that ZBTB4 and ZBTB38 bind methylated DNA in vitro and in vivo. Unlike Kaiso, they can bind single methylated CpGs. - id: zbtb38_variant label: ZBTB38 module_type: MOLECULAR_FUNCTION annotons: - id: zbtb38_methyl_cpg_binding label: ZBTB38 methyl-CpG binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ZBTB38 term: id: UniProtKB:Q8NAP3 label: Zinc finger and BTB domain-containing protein 38 function: preferred_term: methyl-CpG binding term: id: GO:0008327 label: methyl-CpG binding role_description: Kaiso-like reader that represses methylated templates. evidence: - source_id: PMID:16354688 statement: ZBTB4 and ZBTB38 repress methylated templates. supporting_text: ZBTB4 and ZBTB38 repress the transcription of methylated templates in transfection assays. - id: zfp57_variant label: ZFP57 module_type: MOLECULAR_FUNCTION annotons: - id: zfp57_methylated_dna_binding label: ZFP57 methylated TGCCGC binding at imprinting control regions participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ZFP57 term: id: UniProtKB:Q9NU63 label: Zinc finger protein 57 homolog function: preferred_term: double-stranded methylated DNA binding term: id: GO:0010385 label: double-stranded methylated DNA binding processes: - preferred_term: genomic imprinting term: id: GO:0071514 label: genomic imprinting role_description: >- KRAB zinc-finger reader of the methylated allele of imprinting control regions; recruits KAP1/TRIM28, DNMTs and UHRF1 to keep imprints methylated through the preimplantation demethylation wave. evidence: - source_id: PMID:22055183 statement: ZFP57 recognises methylated TGCCGC at ICRs. supporting_text: we identify the methylated TGCCGC hexanucleotide as the motif that is recognized by ZFP57 in all ICRs and in several tens of additional loci - source_id: PMID:22055183 statement: ZFP57 and KAP1 associate with DNMTs and UHRF1 (NP95). supporting_text: Accordingly, we find that ZFP57 and KAP1 associated with DNMTs and hemimethylated DNA-binding NP95. - source_id: PMID:18854139 statement: Zfp57 maintains methylation imprints after fertilisation. supporting_text: Zfp57 is also required for the postfertilization maintenance of maternal and paternal methylation imprints at multiple imprinted domains. connections: - source: de_novo_methylation target: maintenance_methylation connection_type: PROVIDES_INPUT_FOR description: >- De novo patterns are copied through replication: hemimethylated CpG is the UHRF1/DNMT1 substrate. - source: de_novo_methylation target: active_demethylation connection_type: PROVIDES_INPUT_FOR description: 5mC is the TET substrate (RGD edge 5-methylcytosine -> 5-hydroxymethylcytosine). - source: maintenance_methylation target: active_demethylation connection_type: PROVIDES_INPUT_FOR description: Maintained 5mC is equally a TET substrate. - source: de_novo_methylation target: methyl_cpg_reading connection_type: PROVIDES_INPUT_FOR description: Methylated CpG is the ligand of the readers (RGD edge 5-methylcytosine - MBP proteins). - source: maintenance_methylation target: methyl_cpg_reading connection_type: PROVIDES_INPUT_FOR description: Maintained methyl-CpG is read by the same readers. - source: active_demethylation target: maintenance_methylation connection_type: NEGATIVELY_REGULATES description: >- Oxidised cytosines are not maintained, so TET activity also removes methylation passively through replication; TDG/BER removes it actively. knowledge_gaps: - gap_statement: >- Whether E3 ligases other than UHRF1, notably SMARCA3/HLTF, ubiquitinate H3K23 to recruit DNMT1 during maintenance methylation in vivo is not established. boundary: >- SMARCA3 is shown to be an H3K23 ubiquitin ligase stimulated by H3K9me3 that sustains H3K9me3 in colorectal cancer cells; its contribution to DNMT1 recruitment or to the methylation maintained on the daughter strand has not been measured. status: OPEN gap_kind: - BIOLOGY significance: >- A parallel ligase would explain residual maintenance methylation when UHRF1 activity is reduced, and would make SMARCA3 loss in cancer a candidate cause of hypomethylation. provenance: - reference_id: PMID:40680746 supporting_text: While UHRF1-mediated H3 ubiquitination activity is critical for DNMT1 recruitment, recent studies have shown that additional E3 ligases can function in parallel to support this mechanism - gap_statement: >- Whether mammalian cells also remove 5caC by direct decarboxylation to cytosine, without excision and repair, is unresolved; no 5caC decarboxylase has been identified. boundary: >- TDG excision of 5fC and 5caC followed by base excision repair is established and explains the 5caC accumulation in TDG-depleted ES cells; a repair-independent route is proposed but has no assigned enzyme. status: OPEN gap_kind: - BIOLOGY significance: >- A decarboxylase would allow demethylation without strand breaks, which matters for genome stability during the large-scale demethylation of the zygote and primordial germ cells. provenance: - reference_id: PMID:21778364 supporting_text: Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation.