DNA (cytosine-5)-methyltransferase 1 (DNMT1). Maintenance methyltransferase that preferentially methylates hemimethylated DNA to preserve DNA methylation patterns during DNA replication. Catalyzes the transfer of methyl groups to cytosine residues at CpG sites. Essential for genomic imprinting, X-chromosome inactivation, and epigenetic regulation of gene expression.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity Supporting Evidence: file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 is predominantly **nuclear** and **colocalizes with replication foci during S phase**, consistent with replication-coupled maintenance methylation |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity. This is the defining molecular function of Dnmt1. Supporting Evidence: file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 catalyzes transfer of a methyl group to the **C5 position of cytosine** in CpG DNA. file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md The methyl donor is **S-adenosylmethionine (SAM)** (yielding S-adenosylhomocysteine after transfer) |
| GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Transcriptional silencing via CpG-island methylation is a downstream consequence of Dnmt1 maintenance methyltransferase activity, not an independent core function. Reason: Falcon characterizes Dnmt1's primary role as mechanistically narrow (SAM-dependent C5 methyl transfer at hemimethylated CpG); gene silencing via CpG-island methylation is a downstream effect of maintaining the methylation mark rather than a separate core molecular activity. Supporting Evidence: file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 has an intrinsic **preference for hemimethylated CpG DNA** versus unmethylated CpG DNA, consistent with a maintenance role rather than de novo methylation |
| GO:0003677 DNA binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000066774 SUPPORTS TRANSFER Node in PTHR10629 (PANTHER family name "CYTOSINE-SPECIFIC METHYLTRANSFERASE"), the family UniProt also assigns to the target (PTHR10629:SF52). The target is squarely inside the clade and DNA binding is genuinely ancestral for it, so the placement is sound; the term is simply the uninformative parent. MGI:MGI:94912 · mouse Dnmt1 (the review target itself) SUPPORTS TRANSFER The target's own MGI record is one of the two IBD seeds, the expected marker that experimental grounding exists on the target itself: Dnmt1 carries an IDA at this same term (GO:0003677, PMID:11399088), which is among the descendant evidences behind the IBD. UniProtKB:P26358 · human DNMT1 (DNA (cytosine-5)-methyltransferase 1) SUPPORTS TRANSFER The 1:1 human ortholog and the other IBD seed; its DNA binding is not in doubt. The informative claim about how Dnmt1 engages DNA - maintenance methylation of hemimethylated CpG - is carried by GO:0003886 and GO:0141119 elsewhere in this review, which is why the bare parent adds nothing here. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general |
| GO:0003682 chromatin binding | IEA GO_REF:0000002 | ACCEPT | Summary: Chromatin association Reason: Essential for DNMT1 function |
| GO:0003824 catalytic activity | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: catalytic activity Reason: Secondary or downstream function |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: Chromatin association Reason: Essential for DNMT1 function |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: cytoplasm Reason: Secondary or downstream function |
| GO:0006325 chromatin organization | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: chromatin organization Reason: Secondary or downstream function |
| GO:0006346 DNA methylation-dependent constitutive heterochromatin formation | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: DNA methylation-dependent constitutive h... Reason: Secondary or downstream function |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: DNA-templated transcription Reason: Secondary or downstream function |
| GO:0008168 methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity |
| GO:0008270 zinc ion binding | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity |
| GO:0032259 methylation | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: methylation Reason: Secondary or downstream function |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general |
| GO:1903925 response to bisphenol A | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: response to bisphenol A Reason: Secondary or downstream function |
| GO:0005515 protein binding | IPI PMID:10615135 DNA methyltransferase Dnmt1 associates with histone deacetyl... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:10615135 DNA methyltransferase Dnmt1 associates with histone deacetylase activity. |
| GO:0000792 heterochromatin | IEA GO_REF:0000107 | ACCEPT | Summary: heterochromatin Reason: Secondary or downstream function |
| GO:0005654 nucleoplasm | IEA GO_REF:0000107 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0009008 DNA-methyltransferase activity | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: DNA-methyltransferase activity Reason: Secondary or downstream function |
| GO:0010628 positive regulation of gene expression | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: positive regulation of gene expression Reason: Secondary or downstream function |
| GO:0010629 negative regulation of gene expression | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: negative regulation of gene expression Reason: Secondary or downstream function |
| GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Transcriptional silencing via CpG-island methylation is a downstream consequence of Dnmt1 maintenance methyltransferase activity, not an independent core function. Reason: Falcon characterizes Dnmt1's primary role as mechanistically narrow (SAM-dependent C5 methyl transfer at hemimethylated CpG); gene silencing via CpG-island methylation is a downstream effect of maintaining the methylation mark rather than a separate core molecular activity. Supporting Evidence: file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 has an intrinsic **preference for hemimethylated CpG DNA** versus unmethylated CpG DNA, consistent with a maintenance role rather than de novo methylation |
| GO:0140254 histone H3K18ub reader activity | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: histone H3K18ub reader activity Reason: Secondary or downstream function |
| GO:0140257 histone H3K23ub reader activity | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: histone H3K23ub reader activity Reason: Secondary or downstream function |
| GO:0140258 histone H3K14ub reader activity | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: histone H3K14ub reader activity Reason: Secondary or downstream function |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IEA GO_REF:0000107 | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function |
| GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: positive regulation of vascular associat... Reason: Secondary or downstream function |
| GO:1905460 negative regulation of vascular associated smooth muscle cell apoptotic process | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: negative regulation of vascular associat... Reason: Secondary or downstream function |
| GO:1905931 obsolete negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: negative regulation of vascular associat... Reason: Secondary or downstream function |
| GO:1990841 promoter-specific chromatin binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: promoter-specific chromatin binding Reason: Secondary or downstream function |
| GO:0000792 heterochromatin | ISO GO_REF:0000119 | ACCEPT | Summary: heterochromatin Reason: Secondary or downstream function |
| GO:0003677 DNA binding | ISO GO_REF:0000119 | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | ISO GO_REF:0000119 | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity |
| GO:0005654 nucleoplasm | ISO GO_REF:0000119 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0009008 DNA-methyltransferase activity | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: DNA-methyltransferase activity Reason: Secondary or downstream function |
| GO:0010628 positive regulation of gene expression | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: positive regulation of gene expression Reason: Secondary or downstream function |
| GO:0010629 negative regulation of gene expression | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: negative regulation of gene expression Reason: Secondary or downstream function |
| GO:0032991 protein-containing complex | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: protein-containing complex Reason: Secondary or downstream function |
| GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: Transcriptional silencing via CpG-island methylation is a downstream consequence of Dnmt1 maintenance methyltransferase activity, not an independent core function. Reason: Falcon characterizes Dnmt1's primary role as mechanistically narrow (SAM-dependent C5 methyl transfer at hemimethylated CpG); gene silencing via CpG-island methylation is a downstream effect of maintaining the methylation mark rather than a separate core molecular activity. Supporting Evidence: file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 has an intrinsic **preference for hemimethylated CpG DNA** versus unmethylated CpG DNA, consistent with a maintenance role rather than de novo methylation |
| GO:0140254 histone H3K18ub reader activity | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: histone H3K18ub reader activity Reason: Secondary or downstream function |
| GO:0140257 histone H3K23ub reader activity | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: histone H3K23ub reader activity Reason: Secondary or downstream function |
| GO:0140258 histone H3K14ub reader activity | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: histone H3K14ub reader activity Reason: Secondary or downstream function |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | ISO GO_REF:0000119 | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function |
| GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: positive regulation of vascular associat... Reason: Secondary or downstream function |
| GO:1905460 negative regulation of vascular associated smooth muscle cell apoptotic process | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: negative regulation of vascular associat... Reason: Secondary or downstream function |
| GO:1905931 obsolete negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: negative regulation of vascular associat... Reason: Secondary or downstream function |
| GO:1990841 promoter-specific chromatin binding | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: promoter-specific chromatin binding Reason: Secondary or downstream function |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | ISO GO_REF:0000096 | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity |
| GO:0005634 nucleus | ISO GO_REF:0000096 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0009410 response to xenobiotic stimulus | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: response to xenobiotic stimulus Reason: Secondary or downstream function |
| GO:0019904 protein domain specific binding | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: protein domain specific binding Reason: Secondary or downstream function |
| GO:0030331 nuclear estrogen receptor binding | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: nuclear estrogen receptor binding Reason: Secondary or downstream function |
| GO:0034241 positive regulation of macrophage fusion | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: positive regulation of macrophage fusion Reason: Secondary or downstream function |
| GO:0042826 histone deacetylase binding | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: histone deacetylase binding Reason: Secondary or downstream function |
| GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: Transcriptional silencing via CpG-island methylation is a downstream consequence of Dnmt1 maintenance methyltransferase activity, not an independent core function. Reason: Falcon characterizes Dnmt1's primary role as mechanistically narrow (SAM-dependent C5 methyl transfer at hemimethylated CpG); gene silencing via CpG-island methylation is a downstream effect of maintaining the methylation mark rather than a separate core molecular activity. Supporting Evidence: file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 has an intrinsic **preference for hemimethylated CpG DNA** versus unmethylated CpG DNA, consistent with a maintenance role rather than de novo methylation |
| GO:0071560 cellular response to transforming growth factor beta stimulus | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: cellular response to transforming growth... Reason: Secondary or downstream function |
| GO:0010467 gene expression | IMP PMID:21874018 lincRNAs act in the circuitry controlling pluripotency and d... | KEEP AS NON CORE | Summary: gene expression Reason: Secondary or downstream function Supporting Evidence: PMID:21874018 lincRNAs act in the circuitry controlling pluripotency and differentiation. |
| GO:0000792 heterochromatin | IDA PMID:21518897 Structural insight into maintenance methylation by mouse DNA... | ACCEPT | Summary: heterochromatin Reason: Secondary or downstream function Supporting Evidence: PMID:21518897 Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). |
| GO:0000792 heterochromatin | IDA PMID:22323818 Structure-based mechanistic insights into DNMT1-mediated mai... | ACCEPT | Summary: heterochromatin Reason: Secondary or downstream function Supporting Evidence: PMID:22323818 Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. |
| GO:0000792 heterochromatin | IDA PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique... | ACCEPT | Summary: heterochromatin Reason: Secondary or downstream function Supporting Evidence: PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance. |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IDA PMID:21518897 Structural insight into maintenance methylation by mouse DNA... | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity Supporting Evidence: PMID:21518897 Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IDA PMID:22323818 Structure-based mechanistic insights into DNMT1-mediated mai... | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity Supporting Evidence: PMID:22323818 Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. |
| GO:0140254 histone H3K18ub reader activity | IDA PMID:26065575 DNA methylation requires a DNMT1 ubiquitin interacting motif... | KEEP AS NON CORE | Summary: histone H3K18ub reader activity Reason: Secondary or downstream function. Reading ubiquitylated H3 via the RFTS module is a recruitment/activation step supporting the core maintenance methyltransferase activity rather than an independent core function. Supporting Evidence: PMID:26065575 DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination. file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md mono-ubiquitin** marks on **histone H3 (notably H3K18 and H3K23)** and on **PAF15** (a PCNA-associated factor) |
| GO:0140254 histone H3K18ub reader activity | IDA PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique... | KEEP AS NON CORE | Summary: histone H3K18ub reader activity Reason: Secondary or downstream function Supporting Evidence: PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance. |
| GO:0140257 histone H3K23ub reader activity | IDA PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique... | KEEP AS NON CORE | Summary: histone H3K23ub reader activity Reason: Secondary or downstream function Supporting Evidence: PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance. |
| GO:0140258 histone H3K14ub reader activity | IDA PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique... | KEEP AS NON CORE | Summary: histone H3K14ub reader activity Reason: Secondary or downstream function Supporting Evidence: PMID:29053958 Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IDA PMID:21518897 Structural insight into maintenance methylation by mouse DNA... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: This is the core biological process in which Dnmt1's maintenance methyltransferase activity is deployed - copying CpG methylation onto the nascent strand after replication. Supporting Evidence: PMID:21518897 Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 has an intrinsic **preference for hemimethylated CpG DNA** versus unmethylated CpG DNA, consistent with a maintenance role rather than de novo methylation |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IDA PMID:22323818 Structure-based mechanistic insights into DNMT1-mediated mai... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:22323818 Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IMP PMID:17893328 Major and essential role for the DNA methylation mark in mou... | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity Supporting Evidence: PMID:17893328 Sep 24. Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IMP PMID:8898232 De novo DNA cytosine methyltransferase activities in mouse e... | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity Supporting Evidence: PMID:8898232 De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. |
| GO:0005634 nucleus | IMP PMID:17893328 Major and essential role for the DNA methylation mark in mou... | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity Supporting Evidence: PMID:17893328 Sep 24. Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IMP PMID:17893328 Major and essential role for the DNA methylation mark in mou... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:17893328 Sep 24. Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. |
| GO:0106222 lncRNA binding | IDA PMID:25686699 LncRNA Dum interacts with Dnmts to regulate Dppa2 expression... | KEEP AS NON CORE | Summary: lncRNA binding Reason: Secondary or downstream function Supporting Evidence: PMID:25686699 LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. |
| GO:0006346 DNA methylation-dependent constitutive heterochromatin formation | IDA PMID:10615135 DNA methyltransferase Dnmt1 associates with histone deacetyl... | KEEP AS NON CORE | Summary: DNA methylation-dependent constitutive h... Reason: Secondary or downstream function Supporting Evidence: PMID:10615135 DNA methyltransferase Dnmt1 associates with histone deacetylase activity. |
| GO:0008168 methyltransferase activity | IDA PMID:10615135 DNA methyltransferase Dnmt1 associates with histone deacetyl... | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity Supporting Evidence: PMID:10615135 DNA methyltransferase Dnmt1 associates with histone deacetylase activity. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IMP PMID:27892467 Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate cr... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:27892467 Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2. |
| GO:0043045 epigenetic programming of gene expression | IGI PMID:27841881 Transient transcription in the early embryo sets an epigenet... | KEEP AS NON CORE | Summary: epigenetic programming of gene expressio... Reason: Secondary or downstream function Supporting Evidence: PMID:27841881 Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IGI PMID:27841881 Transient transcription in the early embryo sets an epigenet... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:27841881 Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. |
| GO:1903926 cellular response to bisphenol A | IDA PMID:21980460 Gestational exposure to low dose bisphenol A alters social b... | KEEP AS NON CORE | Summary: cellular response to bisphenol A Reason: Secondary or downstream function Supporting Evidence: PMID:21980460 Gestational exposure to low dose bisphenol A alters social behavior in juvenile mice. |
| GO:0005515 protein binding | IPI PMID:17931718 DNMT1 interacts with the developmental transcriptional repre... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:17931718 DNMT1 interacts with the developmental transcriptional repressor HESX1. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IDA PMID:10888872 DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a c... | KEEP AS NON CORE | Summary: negative regulation of transcription by ... Reason: Secondary or downstream function Supporting Evidence: PMID:10888872 DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. |
| GO:0009008 DNA-methyltransferase activity | TAS Reactome:R-MMU-573383 | KEEP AS NON CORE | Summary: DNA-methyltransferase activity Reason: Secondary or downstream function |
| GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates | TAS Reactome:R-MMU-5336369 | KEEP AS NON CORE | Summary: DNA (cytosine-5-)-methyltransferase acti... Reason: Secondary or downstream function |
| GO:0043045 epigenetic programming of gene expression | IMP PMID:29117290 The DNA Methyltransferase 1 (DNMT1) Controls the Shape and D... | KEEP AS NON CORE | Summary: epigenetic programming of gene expressio... Reason: Secondary or downstream function Supporting Evidence: PMID:29117290 The DNA Methyltransferase 1 (DNMT1) Controls the Shape and Dynamics of Migrating POA-Derived Interneurons Fated for the Murine Cerebral Cortex. |
| GO:0009008 DNA-methyltransferase activity | IMP PMID:1606615 Targeted mutation of the DNA methyltransferase gene results ... | KEEP AS NON CORE | Summary: DNA-methyltransferase activity Reason: Secondary or downstream function Supporting Evidence: PMID:1606615 Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. |
| GO:0043045 epigenetic programming of gene expression | IMP PMID:1606615 Targeted mutation of the DNA methyltransferase gene results ... | KEEP AS NON CORE | Summary: epigenetic programming of gene expressio... Reason: Secondary or downstream function Supporting Evidence: PMID:1606615 Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. |
| GO:1990841 promoter-specific chromatin binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: promoter-specific chromatin binding Reason: Secondary or downstream function |
| GO:0005515 protein binding | IPI PMID:24335282 Analysis of the SWI/SNF chromatin-remodeling complex during ... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:24335282 Dec 13. Analysis of the SWI/SNF chromatin-remodeling complex during early heart development and BAF250a repression cardiac gene transcription during P19 cell differentiation. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:24105743 Oncogenic RAS directs silencing of tumor suppressor genes th... | KEEP AS NON CORE | Summary: negative regulation of transcription by ... Reason: Secondary or downstream function Supporting Evidence: PMID:24105743 Oct 8. Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors. |
| GO:0003682 chromatin binding | IDA PMID:24105743 Oncogenic RAS directs silencing of tumor suppressor genes th... | ACCEPT | Summary: Chromatin association Reason: Essential for DNMT1 function Supporting Evidence: PMID:24105743 Oct 8. Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IMP PMID:24105743 Oncogenic RAS directs silencing of tumor suppressor genes th... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:24105743 Oct 8. Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors. |
| GO:0005634 nucleus | IDA PMID:16424344 Methylation of tRNAAsp by the DNA methyltransferase homolog ... | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity Supporting Evidence: PMID:16424344 Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:16887828 DNA methylation is a primary mechanism for silencing postmig... | KEEP AS NON CORE | Summary: negative regulation of transcription by ... Reason: Secondary or downstream function Supporting Evidence: PMID:16887828 DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IMP PMID:16887828 DNA methylation is a primary mechanism for silencing postmig... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:16887828 DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. |
| GO:0010468 regulation of gene expression | IMP PMID:23028046 Cellular adaptation to anthrax lethal toxin-induced mitochon... | KEEP AS NON CORE | Summary: regulation of gene expression Reason: Secondary or downstream function Supporting Evidence: PMID:23028046 Oct 1. Cellular adaptation to anthrax lethal toxin-induced mitochondrial cholesterol enrichment, hyperpolarization, and reactive oxygen species generation through downregulating MLN64 in macrophages. |
| GO:0005515 protein binding | IPI PMID:17994007 The SRA protein Np95 mediates epigenetic inheritance by recr... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:17994007 The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. |
| GO:0005515 protein binding | IPI PMID:21268065 Usp7 and Uhrf1 control ubiquitination and stability of the m... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:21268065 Usp7 and Uhrf1 control ubiquitination and stability of the maintenance DNA methyltransferase Dnmt1. |
| GO:0003723 RNA binding | IDA PMID:20573698 Kcnq1ot1 noncoding RNA mediates transcriptional gene silenci... | KEEP AS NON CORE | Summary: RNA binding Reason: Secondary or downstream function Supporting Evidence: PMID:20573698 Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. |
| GO:0008327 methyl-CpG binding | IDA PMID:20573698 Kcnq1ot1 noncoding RNA mediates transcriptional gene silenci... | KEEP AS NON CORE | Summary: methyl-CpG binding Reason: Secondary or downstream function Supporting Evidence: PMID:20573698 Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. |
| GO:0071230 cellular response to amino acid stimulus | IDA PMID:20548288 Difference in expression of hepatic microRNAs miR-29c, miR-3... | KEEP AS NON CORE | Summary: cellular response to amino acid stimulus Reason: Secondary or downstream function Supporting Evidence: PMID:20548288 2010 Jun 14. Difference in expression of hepatic microRNAs miR-29c, miR-34a, miR-155, and miR-200b is associated with strain-specific susceptibility to dietary nonalcoholic steatohepatitis in mice. |
| GO:0005654 nucleoplasm | TAS Reactome:R-MMU-5336365 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0005654 nucleoplasm | TAS Reactome:R-MMU-5336369 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0005654 nucleoplasm | TAS Reactome:R-MMU-573336 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0005654 nucleoplasm | TAS Reactome:R-MMU-573376 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0005654 nucleoplasm | TAS Reactome:R-MMU-573383 | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity |
| GO:0005515 protein binding | IPI PMID:16085498 The PHD finger/bromodomain of NoRC interacts with acetylated... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:16085498 The PHD finger/bromodomain of NoRC interacts with acetylated histone H4K16 and is sufficient for rDNA silencing. |
| GO:0005515 protein binding | IPI PMID:15550930 Replication-independent chromatin loading of Dnmt1 during G2... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:15550930 Replication-independent chromatin loading of Dnmt1 during G2 and M phases. |
| GO:0005721 pericentric heterochromatin | IDA PMID:17576694 Dynamics of Dnmt1 interaction with the replication machinery... | KEEP AS NON CORE | Summary: pericentric heterochromatin Reason: Secondary or downstream function Supporting Evidence: PMID:17576694 Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. |
| GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation | IMP PMID:17576694 Dynamics of Dnmt1 interaction with the replication machinery... | KEEP AS NON CORE | Summary: Transcriptional silencing via CpG-island methylation is a downstream consequence of Dnmt1 maintenance methyltransferase activity, not an independent core function. Reason: Falcon characterizes Dnmt1's primary role as mechanistically narrow (SAM-dependent C5 methyl transfer at hemimethylated CpG); gene silencing via CpG-island methylation is a downstream effect of maintaining the methylation mark rather than a separate core molecular activity. Supporting Evidence: PMID:17576694 Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. |
| GO:0042127 regulation of cell population proliferation | IGI PMID:10919675 Dnmt1N/+ reduces the net growth rate and multiplicity of int... | KEEP AS NON CORE | Summary: regulation of cell population proliferat... Reason: Secondary or downstream function Supporting Evidence: PMID:10919675 Dnmt1N/+ reduces the net growth rate and multiplicity of intestinal adenomas in C57BL/6-multiple intestinal neoplasia (Min)/+ mice independently of p53 but demonstrates strong synergy with the modifier of Min 1(AKR) resistance allele. |
| GO:0005634 nucleus | IDA PMID:17931718 DNMT1 interacts with the developmental transcriptional repre... | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity Supporting Evidence: PMID:17931718 DNMT1 interacts with the developmental transcriptional repressor HESX1. |
| GO:0010468 regulation of gene expression | IMP PMID:16491076 Negative regulation of CD8 expression via Cd8 enhancer-media... | KEEP AS NON CORE | Summary: regulation of gene expression Reason: Secondary or downstream function Supporting Evidence: PMID:16491076 Negative regulation of CD8 expression via Cd8 enhancer-mediated recruitment of the zinc finger protein MAZR. |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:17245608 A developmental window of opportunity for imprinted gene sil... | KEEP AS NON CORE | Summary: negative regulation of DNA-templated tra... Reason: Secondary or downstream function Supporting Evidence: PMID:17245608 Jan 23. A developmental window of opportunity for imprinted gene silencing mediated by DNA methylation and the Kcnq1ot1 noncoding RNA. |
| GO:0005515 protein binding | IPI PMID:10888872 DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a c... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:10888872 DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. |
| GO:0005657 replication fork | IDA PMID:10888872 DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a c... | ACCEPT | Summary: replication fork Reason: Dnmt1 localizes to replication foci/forks during S phase, the site where it performs replication-coupled maintenance methylation. Core to its mechanism. Supporting Evidence: PMID:10888872 DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md DNMT1 is predominantly **nuclear** and **colocalizes with replication foci during S phase**, consistent with replication-coupled maintenance methylation |
| GO:0005634 nucleus | IDA PMID:15063176 Windows for sex-specific methylation marked by DNA methyltra... | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity Supporting Evidence: PMID:15063176 Windows for sex-specific methylation marked by DNA methyltransferase expression profiles in mouse germ cells. |
| GO:0000792 heterochromatin | IDA PMID:14519686 Analysis of mammalian proteins involved in chromatin modific... | ACCEPT | Summary: heterochromatin Reason: Secondary or downstream function Supporting Evidence: PMID:14519686 Sep 30. Analysis of mammalian proteins involved in chromatin modification reveals new metaphase centromeric proteins and distinct chromosomal distribution patterns. |
| GO:0005634 nucleus | IDA PMID:11942627 Expression of DNA methyltransferase (Dnmt1) in testicular ge... | ACCEPT | Summary: Nuclear localization Reason: Essential site of DNMT1 activity Supporting Evidence: PMID:11942627 Expression of DNA methyltransferase (Dnmt1) in testicular germ cells during development of mouse embryo. |
| GO:0003677 DNA binding | IDA PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is co... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general. Dnmt1 DNA binding is better captured by its specific preference for hemimethylated CpG (maintenance) and CXXC-mediated unmethylated-CpG binding that contributes to autoinhibition, rather than generic DNA binding. Supporting Evidence: PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. file:mouse/Dnmt1/Dnmt1-deep-research-falcon.md CXXC-linked autoinhibitory mechanism further helps prevent inappropriate methylation of unmethylated CpGs |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IDA PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is co... | ACCEPT | Summary: Core methyltransferase function Reason: Essential DNMT1 enzymatic activity Supporting Evidence: PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. |
| GO:0008270 zinc ion binding | IDA PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is co... | MARK AS OVER ANNOTATED | Summary: Non-specific term Reason: Term is too general Supporting Evidence: PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | IDA PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is co... | ACCEPT | Summary: chromosomal DNA methylation maintenance ... Reason: Secondary or downstream function Supporting Evidence: PMID:11399088 The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. |
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