MET1A (OsMET1a / OsMET1-1; UniProt Q7Y1I7; LOC_Os03g58400 / Os03g0798300) is a rice DNMT1-like maintenance DNA (cytosine-5) methyltransferase (EC 2.1.1.37). Its core molecular function is the S-adenosyl-L-methionine-dependent transfer of a methyl group to the C5 position of cytosine in DNA, acting primarily at symmetric CG (CpG) sites to copy methylation patterns onto the nascent strand after DNA replication - i.e. maintenance CG methylation underpinning epigenetic inheritance. The protein has the canonical DNMT1 architecture: two N-terminal RFTS/replication-foci-targeting regions, two BAH (bromo-adjacent homology) chromatin-reading domains, and a C-terminal SAM-dependent C5 methyltransferase catalytic domain with the conserved active-site cysteine (Act_site 1197). Rice carries two closely related MET1 paralogs, OsMET1a (OsMET1-1, this gene) and OsMET1b (OsMET1-2). Both contain all binding and catalytic domains required for a functional CG methylase, but OsMET1b is the dominant, far more highly expressed enzyme: ribonuclease protection assays show steady-state OsMET1-2 mRNA is 7- to 12-fold higher than OsMET1-1 in callus, root and inflorescence [PMID:14513380], and an OsMET1-1 knock-in mutant produces no discernible developmental phenotype, indicating a minor and/or redundant role for OsMET1a in CG-methylation maintenance compared with OsMET1b [file:ORYSJ/MET1A/MET1A-deep-research-falcon.md]. The most quantitative causal data for the rice MET1 pathway come from loss of the major paralog OsMET1b, where gene-body mCG falls ~86% (27.35% to 3.95%), transposon mCG falls ~77%, transposons are derepressed, and OsMET1a is transcriptionally induced ~2.5-fold together with a VIM-like cofactor (~4.5-fold) - placing OsMET1a squarely in the CG maintenance machinery and its compensatory/buffering responses [file:ORYSJ/MET1A/MET1A-deep-research-falcon.md]. MET1A acts in the nucleus on chromosomal DNA. By maintaining CG methylation it contributes (secondarily) to transposon/heterochromatin silencing and methylation-dependent gene silencing, but its defining role is the maintenance methyltransferase reaction itself, not a particular downstream regulatory outcome. Direct in vitro biochemical assays of OsMET1a substrate preference and a dedicated subcellular localization experiment have not been reported; nuclear localization (UniProt, ECO:0000305) and CG specificity are inferred from the enzyme class, domain architecture, and the rice MET1 genetics literature.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation propagated across the DNMT1/MET1 phylogenetic group. As a DNA (cytosine-5) methyltransferase acting on chromosomal DNA, MET1A functions in the nucleus. Reason: Core cellular-component annotation and well supported. UniProt assigns MET1A to the nucleus (ECO:0000305), consistent with a maintenance DNA methyltransferase that copies CG methylation onto chromosomal DNA during/after replication. The deep-research synthesis reaches the same conclusion. The IBA term is at the correct level of specificity. Supporting Evidence: file:ORYSJ/MET1A/MET1A-deep-research-falcon.md Based on its demonstrated role as a DNA methyltransferase maintaining genomic CG methylation, its functional site of action is most plausibly the **nucleus** |
| GO:0003677 DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation propagated from the DNMT1/MET1 group. MET1A binds DNA: it is a DNA-dependent enzyme whose substrate is double-stranded (hemimethylated) genomic DNA. Reason: Correct and supported by the protein's enzyme class and domain architecture (DNA-binding keyword in UniProt; C5-methyltransferase catalytic domain acting on DNA). DNA binding is a generic term but it is not wrong; the more informative molecular function is the cytosine-5 methyltransferase activity (GO:0003886, retained below). Accept the IBA DNA-binding annotation. Supporting Evidence: PMID:14513380 each encoding a cytosine-5 DNA methyltransferase (MTase) file:ORYSJ/MET1A/MET1A-deep-research-falcon.md OsMET1-1 and OsMET1-2 are highly similar and contain all **binding and catalytic domains required for a functional CG methylase** |
| GO:0003682 chromatin binding | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro (IPR001025, BAH domain). MET1A contains two BAH (bromo-adjacent homology) domains, chromatin-reading modules of DNMT1/MET1 enzymes. Reason: Supported by domain content. UniProt annotates two BAH domains (residues 742-874 and 910-1049) in MET1A, and the InterPro BAH-to-GO mapping assigns chromatin binding. BAH domains in DNMT1/MET1 read chromatin/nucleosome marks to target maintenance methylation to replicating heterochromatin, so chromatin binding is an appropriate, if generic, molecular-function annotation for this enzyme. Supporting Evidence: file:ORYSJ/MET1A/MET1A-deep-research-falcon.md UniProt/domain annotation for Q7Y1I7 further supports a DNMT1-like architecture with **BAH** and **C5-methyltransferase** domains |
| GO:0003886 DNA (cytosine-5-)-methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation (RHEA:13681 / EC 2.1.1.37). This is the defining, core molecular function of MET1A: SAM-dependent transfer of a methyl group to C5 of cytosine in DNA. Reason: This is the core molecular function and is strongly supported. UniProt assigns EC 2.1.1.37 with the explicit catalytic reaction (a 2'-deoxycytidine in DNA + SAM = a 5-methyl-2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H+), and the protein belongs to the class I-like SAM-binding methyltransferase superfamily, C5-methyltransferase family, with the conserved active-site cysteine at position 1197. The biochemical paper describes OsMET1-1 directly as a cytosine-5 DNA methyltransferase. This is precisely the activity that the bare retired keyword term "methylation" (GO:0032259) failed to capture. Supporting Evidence: PMID:14513380 each encoding a cytosine-5 DNA methyltransferase (MTase) file:ORYSJ/MET1A/MET1A-deep-research-falcon.md MET1A is annotated as a SAM-dependent **DNA (cytosine-5) methyltransferase (EC 2.1.1.37)** that transfers a methyl group to the **C5 position of cytosine** in DNA |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation derived from the UniProtKB/Swiss-Prot subcellular-location mapping (SL-0191, Nucleus); duplicates the IBA nucleus annotation. Reason: Correct and consistent with the IBA nucleus annotation and with the UniProt subcellular location (Nucleus, ECO:0000305). Duplicate cellular-component annotations with different evidence codes are acceptable. A maintenance DNA methyltransferase acts on chromosomal DNA in the nucleus. Supporting Evidence: file:ORYSJ/MET1A/MET1A-deep-research-falcon.md a DNA methyltransferase acting on chromosomal DNA is most plausibly **nuclear** |
| GO:0008168 methyltransferase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: IEA annotation from InterPro (IPR001525, C5_MeTfrase). "Methyltransferase activity" is the high-level parent of the gene's specific DNA (cytosine-5) methyltransferase activity. Reason: "Methyltransferase activity" is a broad grouping term. MET1A is a methyltransferase, so the term is not wrong, but it is uninformative once the specific child term DNA (cytosine-5-)- methyltransferase activity (GO:0003886, retained above) is present - the specific term drops both the substrate (DNA) and the position (C5 of cytosine). Retaining a bare "methyltransferase activity" alongside the specific MF adds no information. Mark as over-annotated; the specific MF is the one to keep. Supporting Evidence: file:ORYSJ/MET1A/MET1A-deep-research-falcon.md MET1A is annotated as a SAM-dependent **DNA (cytosine-5) methyltransferase (EC 2.1.1.37)** that transfers a methyl group to the **C5 position of cytosine** in DNA |
| GO:0045814 negative regulation of gene expression, epigenetic | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: IEA annotation (ARBA machine-learning model). CG methylation by MET1 contributes to epigenetic gene silencing, but this is a downstream consequence rather than MET1A's defining function. Reason: Biologically reasonable but non-core. Maintenance CG methylation by MET1 enzymes contributes to methylation-dependent epigenetic gene silencing - RNAi knockdown of OsMET1-1 reactivated a silenced transgene, consistent with the involvement of maintenance methylation in silencing [PMID:14513380]. However, "negative regulation of gene expression, epigenetic" is a pleiotropic downstream outcome of the enzyme's activity, not the molecular reaction the gene product carries out. Keep, but mark as non-core; the core annotation is the methyltransferase activity and the maintenance-methylation process. Supporting Evidence: PMID:14513380 Restoration of uidA expression in the bombarded calli was consistent with the inactivation of maintenance methylation and with previous evidence for the involvement of methylation in silencing of this line. file:ORYSJ/MET1A/MET1A-deep-research-falcon.md linking CG maintenance methylation to TE repression and transcriptome stability |
| GO:0006346 DNA methylation-dependent constitutive heterochromatin formation | IMP PMID:14513380 Characterization of two rice DNA methyltransferase genes and... | KEEP AS NON CORE | Summary: IMP annotation citing PMID:14513380. RNAi knockdown of OsMET1-1 in rice callus reactivated a methylation-silenced transgene, implicating MET1A-mediated maintenance methylation in heterochromatin/silencing - a downstream contribution rather than the core enzymatic role. Reason: The annotation is reasonably supported by the cited reference but represents a secondary role. Teerawanichpan et al. used RNAi inverted-repeat constructs against OsMET1-1 and restored expression of a silenced 35S-uidA-nos transgene, consistent with loss of maintenance methylation [PMID:14513380]. MET1-mediated CG maintenance does contribute to transposon/heterochromatin silencing (loss of the major paralog OsMET1b causes broad transposon derepression). However, OsMET1a is the minor paralog (7-12x lower expression; no knock-in phenotype), and constitutive-heterochromatin formation is a downstream, pleiotropic consequence of CG maintenance rather than MET1A's defining function. Keep as non-core; the core process is maintenance CG methylation (see the SPKW MODIFY entry to GO:0141119). Supporting Evidence: PMID:14513380 Restoration of uidA expression in the bombarded calli was consistent with the inactivation of maintenance methylation and with previous evidence for the involvement of methylation in silencing of this line. PMID:14513380 the steady-state level of OsMET1-2 was 7- to 12-fold higher than that for OsMET1-1 in callus, root and inflorescence |
| GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS annotation transferred from human DNMT1 (UniProtKB:P34881). CG methylation by MET1A can repress gene expression at CpG-rich regions, but the CpG-island concept is mammalian and this is a downstream regulatory outcome, not the core function. Reason: The essence (CG methylation leading to transcriptional repression) is consistent with MET1 biology - maintenance CG methylation is associated with silencing, and RNAi of OsMET1-1 reactivated a methylation-silenced transgene [PMID:14513380]. However, the term is an ISS transfer from human DNMT1 framed around mammalian "CpG islands" (gene-promoter CG-dense regions), a concept that does not map cleanly onto plant genome methylation, where CG, CHG and CHH methylation predominate over much of the genome including transposons. It is best retained as a non-core, similarity-based annotation describing a downstream regulatory consequence rather than MET1A's defining maintenance-methyltransferase reaction. Supporting Evidence: PMID:14513380 Restoration of uidA expression in the bombarded calli was consistent with the inactivation of maintenance methylation and with previous evidence for the involvement of methylation in silencing of this line. file:ORYSJ/MET1A/MET1A-deep-research-falcon.md OsMET1a is described as a **maintenance DNA methyltransferase responsible for CG methylation** |
| GO:0032259 methylation | IEA GO_REF:0000043 | MODIFY | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Methyltransferase"; snapshot-only, removed in the current GOA release. "Methylation" (GO:0032259) is the bare, substrate-agnostic process term ("a methyl group is covalently attached to a molecule") - it drops the substrate (DNA), the position (C5 of cytosine) and the maintenance specificity that define MET1A. Reason: This is the classic enzyme-class-keyword -> bare-process conflation (Tier A). MET1A is a DNA (cytosine-5) methyltransferase (EC 2.1.1.37) whose specific biological process is maintenance of CG DNA methylation after replication, not generic "methylation". The generic term GO:0032259 is uninformative: it would equally fit a protein, RNA, or small-molecule methyltransferase. The substrate-specific, MET1-specific process term is GO:0141119 "chromosomal DNA methylation maintenance following DNA replication", whose GO definition explicitly states that CG methylation is maintained by "a maintenance DNA methyltransferase called DNMT1 in mammals and MET1 (DNA METHYLTRANSFERASE 1) in plants" together with the VIM cofactor - matching OsMET1a exactly (including the ~4.5-fold VIM co-induction seen when the major paralog OsMET1b is lost). NOTE: the older generic process terms "DNA methylation" (GO:0006306) and "maintenance of DNA methylation"-type "negative regulation of gene expression via chromosomal DNA cytosine methylation" (GO:0010216) are now OBSOLETE in the authoritative GO release, so GO:0141119 is the correct non-obsolete replacement. Removing the bare keyword term loses nothing of value, but the underlying maintenance-methylation biology should be captured by GO:0141119, so a MODIFY (rather than a plain MARK_AS_OVER_ANNOTATED) is the right action. Tier A. Proposed replacements: chromosomal DNA methylation maintenance following DNA replication Supporting Evidence: PMID:14513380 Restoration of uidA expression in the bombarded calli was consistent with the inactivation of maintenance methylation and with previous evidence for the involvement of methylation in silencing of this line. file:ORYSJ/MET1A/MET1A-deep-research-falcon.md Maintenance methylation refers to the **copying of symmetric methylation patterns (especially CG) onto the nascent strand following semi-conservative DNA replication**, enabling epigenetic inheritance across cell divisions. In rice, **CG methylation is mainly maintained by MET1 enzymes**, specifically **OsMET1a (OsMET1-1)** and **OsMET1b (OsMET1-2)** file:ORYSJ/MET1A/MET1A-deep-research-falcon.md MET1A is annotated as a SAM-dependent **DNA (cytosine-5) methyltransferase (EC 2.1.1.37)** that transfers a methyl group to the **C5 position of cytosine** in DNA, primarily maintaining **CG methylation** |
| GO:0141119 chromosomal DNA methylation maintenance following DNA replication | ISS file:ORYSJ/MET1A/MET1A-deep-research-falcon.md | NEW | Summary: Proposed substrate-specific process annotation capturing MET1A's core biological role: maintenance of symmetric CG methylation by copying the parental methylation pattern onto the newly replicated strand. This is the precise term that should replace the retired bare "methylation" (GO:0032259) keyword annotation. Reason: MET1A is a DNMT1/MET1-class maintenance CG methyltransferase. The GO definition of GO:0141119 names MET1 in plants as the maintenance DNA methyltransferase and VIM as its cofactor, exactly matching the rice MET1a biology synthesized in the deep-research report (OsMET1a/OsMET1b maintain CG methylation; loss of the major paralog OsMET1b collapses gene-body mCG from 27.35% to 3.95% and co-induces OsMET1a ~2.5-fold and a VIM-like factor ~4.5-fold). The current GOA has no substrate-specific maintenance-methylation process term for MET1A; this is the appropriate, non-obsolete replacement for the generic SPKW "methylation" term. ISS is used because rice OsMET1a-specific in vitro/in vivo maintenance assays were not retrieved; the assignment rests on enzyme class, DNMT1-like domain architecture (RFTS + BAH + C5-MTase), and orthology to characterized MET1/DNMT1 maintenance methyltransferases. Supporting Evidence: file:ORYSJ/MET1A/MET1A-deep-research-falcon.md Maintenance methylation refers to the **copying of symmetric methylation patterns (especially CG) onto the nascent strand following semi-conservative DNA replication**, enabling epigenetic inheritance across cell divisions. In rice, **CG methylation is mainly maintained by MET1 enzymes**, specifically **OsMET1a (OsMET1-1)** and **OsMET1b (OsMET1-2)** PMID:14513380 each encoding a cytosine-5 DNA methyltransferase (MTase) |
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Download this section (compressed HTML)Q: Does rice OsMET1a have intrinsic maintenance CG-methyltransferase activity in vitro, and does it preferentially methylate hemimethylated CG substrates as expected for a DNMT1/MET1 maintenance enzyme?
Suggested experts: Bao Liu
Q: What is the division of labour between OsMET1a and the dominant paralog OsMET1b - is OsMET1a a genuine backup maintenance methylase induced when OsMET1b is lost, or does it have locus- or tissue-specific maintenance targets?
Suggested experts: Xiaofeng Cao
Experiment: Express and purify recombinant OsMET1a and assay SAM-dependent methyl transfer on hemimethylated versus unmethylated CG, CHG and CHH oligonucleotide substrates to confirm maintenance CG specificity directly.
Hypothesis: OsMET1a is a maintenance methyltransferase with strong preference for hemimethylated CG (CpG) sites, consistent with the DNMT1/MET1 class.
Type: in vitro methyltransferase activity assay
Experiment: Generate clean osmet1a single and osmet1a osmet1b double knockouts (e.g. by CRISPR) and perform whole-genome bisulfite sequencing to quantify the CG-methylation contribution attributable specifically to OsMET1a, including in the OsMET1b-deficient background where OsMET1a is induced.
Hypothesis: OsMET1a makes a measurable but minor contribution to genome-wide CG maintenance that becomes detectable (or essential) only when OsMET1b is absent.
Type: genetic knockout combined with whole-genome bisulfite sequencing
Experiment: Determine the subcellular localization and replication-coupling of OsMET1a using a functional OsMET1a-GFP fusion and co-localization with replication-fork/PCNA markers in dividing rice cells.
Hypothesis: OsMET1a localizes to the nucleus and is recruited to replication foci during S phase, consistent with a replication-coupled maintenance methyltransferase.
Type: fluorescent-protein localization and replication co-localization assay
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