| Category | Direct evidence for OsMET1a/MET1A | Inference / context (clearly labeled) | Key sources (year; DOI/URL) |
|---|---|---|---|
| Identity / synonyms | UniProt target Q7Y1I7 is rice **DNA (cytosine-5)-methyltransferase 1A**, short name **OsMET1a**; gene **MET1A**; synonyms **MET1-1 / OsMET1-1**; loci **Os03g0798300 / LOC_Os03g58400**. Rice literature distinguishes **OsMET1-1 (OsMET1a)** from **OsMET1-2 (OsMET1b)**, confirming the target is the OsMET1-1 paralog, not a different MET1 gene (pqac-00000001, pqac-00000004, pqac-00000007) | Because the literature repeatedly maps OsMET1a to LOC_Os03g58400 and contrasts it with OsMET1-2, the symbol is sufficiently disambiguated for functional annotation of Q7Y1I7 (pqac-00000001, pqac-00000004) | Hu et al. 2014, PNAS, DOI: 10.1073/pnas.1410761111, https://doi.org/10.1073/pnas.1410761111 (pqac-00000001); Kumar et al. 2022, Front Plant Sci, DOI: 10.3389/fpls.2022.871890, https://doi.org/10.3389/fpls.2022.871890 (pqac-00000004); Yin et al. 2024, Plants, DOI: 10.3390/plants13192700, https://doi.org/10.3390/plants13192700 (pqac-00000007) |
| Molecular function & reaction | Rice MET1 proteins are described as **maintenance CG methyltransferases**; OsMET1a/OsMET1-1 is identified as a maintenance DNA methyltransferase responsible for **CG methylation**. Hu et al. state OsMET1-1 and OsMET1-2 contain all binding and catalytic domains required for a functional CG methylase; Kumar et al. identify OsMET1a as MET1 responsible for CG methylation (pqac-00000001, pqac-00000004, pqac-00000007) | The exact catalytic chemistry for Q7Y1I7 is inferred from the MET1/C5-methyltransferase class and UniProt family/domain assignment: **SAM-dependent transfer of a methyl group to C5 of cytosine in DNA**, acting primarily at **hemimethylated CG sites after replication**. This is consistent with general MET1 biology described in recent reviews, but a rice OsMET1a-specific biochemical assay was not retrieved here (pqac-00000007, pqac-00000010) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000001); Kumar et al. 2022, https://doi.org/10.3389/fpls.2022.871890 (pqac-00000004); Yin et al. 2024, https://doi.org/10.3390/plants13192700 (pqac-00000007); Qiao et al. 2024, https://doi.org/10.3390/agronomy15010094 (pqac-00000010) |
| Domains / family | Hu et al. report that OsMET1-1 and OsMET1-2 are highly similar and contain all **binding and catalytic domains required for a functional CG methylase** (pqac-00000001) | UniProt/domain annotation for Q7Y1I7 further supports a DNMT1-like architecture with **BAH** and **C5-methyltransferase** domains, consistent with a class I-like SAM-binding methyltransferase; this supports maintenance-methylase function when direct domain mapping from primary papers is limited in the retrieved evidence (pqac-00000001) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000001) |
| Expression pattern / relative importance | In WT rice tissues, **OsMET1-2 transcripts accumulated more abundantly than OsMET1-1 in all examined tissues**, implying OsMET1a is the lower-expressed paralog. A reported **OsMET1-1 knock-in mutant failed to show discernible developmental phenotypes**, suggesting a minimal and/or redundant role relative to OsMET1-2 (pqac-00000001, pqac-00000011) | The cited but not directly retrieved Yamauchi et al. study is described as showing **dosage-dependent spatiotemporal expression** of MET1a, indicating expression and/or phenotype may depend on gene dosage and developmental context, but detailed primary data were not available in the conversation evidence (pqac-00000006, pqac-00000012) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000001, pqac-00000011); Li et al. 2021, https://doi.org/10.1186/s12864-021-07600-7 (pqac-00000006); Terada et al. 2010, https://doi.org/10.5511/plantbiotechnology.27.29 (pqac-00000012) |
| Pathways / partners: VIM | In OsMET1-2 knockout seedlings, a rice **VIM-family gene** (LOC_Os05g01230) was upregulated about **4.5-fold**; the paper notes VIM proteins cooperate with CG methylases to maintain CG methylation (pqac-00000002) | Direct physical interaction between **OsMET1a** and a rice VIM protein was not shown in the retrieved evidence. The partner relationship is therefore supported as **pathway-level inference** from MET1/VIM cooperation in CG maintenance and compensatory responses in rice MET1 mutants (pqac-00000002, pqac-00000010) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000002); Qiao et al. 2024, https://doi.org/10.3390/agronomy15010094 (pqac-00000010) |
| Pathways / partners: RdDM | Rice MET1 function is linked to **RNA-directed DNA methylation (RdDM)**. Hu et al. propose residual/regained mCG in an OsMET1-2 mutant may be maintained partly via RdDM, especially in heterochromatic TE-rich regions; altered 24-nt small RNAs and CHH methylation support MET1–RdDM interplay (pqac-00000002, pqac-00000005) | For **OsMET1a specifically**, RdDM involvement is inferential rather than directly demonstrated. Recent rice reviews state CHH methylation is controlled by RdDM, and MET1-mediated CG maintenance interacts with broader methylation pathways and TE silencing networks (pqac-00000007, pqac-00000009) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000002, pqac-00000005); Yin et al. 2024, https://doi.org/10.3390/plants13192700 (pqac-00000007, pqac-00000009) |
| Pathways / partners: DDM1 / chromatin context | Recent rice review evidence states **DDM1-dependent methylation** and **RdDM** can compensate to maintain TE silencing; DDM1 is essential for cytosine methylation in repeats/TEs in rice and acts independently of siRNA at some loci (pqac-00000007) | No direct OsMET1a–DDM1 interaction was shown in the retrieved OsMET1a-specific studies. The relationship is best described as **shared participation in the rice DNA methylation / heterochromatin maintenance network** (pqac-00000007, pqac-00000009) | Yin et al. 2024, https://doi.org/10.3390/plants13192700 (pqac-00000007, pqac-00000009) |
| Key quantitative findings relevant to MET1 pathway | In **OsMET1-2** mutants, **OsMET1-1 expression increased ~2.5-fold**, VIM gene expression increased ~4.5-fold, gene-body **mCG fell 86% (27.35% to 3.95%)**, TE mCG fell **77%**, and **89%** of hypo-differentially methylated cytosines were in CG context; **594/2,716 TEs (21.9%)** changed expression, with **489 (82.3%) upregulated** (pqac-00000002, pqac-00000003, pqac-00000005, pqac-00000013) | These quantitative data come from mutation of the **major paralog OsMET1-2**, not direct disruption of OsMET1a. They are nevertheless informative for annotating OsMET1a because OsMET1a is transcriptionally induced in this background and belongs to the same maintenance-CG pathway (pqac-00000002, pqac-00000003) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000002, pqac-00000003, pqac-00000005, pqac-00000013) |
| Stress-responsive regulation / applications relevance | Under phosphate starvation, **OsMET1a promoter hypomethylation correlated with increased OsMET1a expression** in roots of the tolerant NIL-23 line, whereas promoter hypermethylation correlated with lower expression in Pusa-44; this supports stress-responsive transcriptional regulation of OsMET1a (pqac-00000004) | This study supports OsMET1a as a responsive node in stress-associated methylation circuitry, but it does **not** directly prove OsMET1a is causal for phosphate tolerance. It is better interpreted as evidence for regulatory responsiveness of the CG-maintenance system under nutrient stress (pqac-00000004, pqac-00000007) | Kumar et al. 2022, https://doi.org/10.3389/fpls.2022.871890 (pqac-00000004); Yin et al. 2024, https://doi.org/10.3390/plants13192700 (pqac-00000007) |
| Overall functional annotation conclusion | Direct evidence supports annotating Q7Y1I7/OsMET1a as a **rice nuclear DNA cytosine-5 maintenance methyltransferase for CG methylation**, acting in epigenetic inheritance and genome/TE regulation, with lower expression and apparently more redundant contribution than OsMET1-2 (pqac-00000001, pqac-00000004, pqac-00000007, pqac-00000011) | Localization was not directly shown in the retrieved OsMET1a papers, but a DNA methyltransferase acting on chromosomal DNA is most plausibly **nuclear**; this should be labeled as inference unless a localization experiment is cited. Recent applications are broader crop epigenetics/epigenome-editing concepts rather than OsMET1a-targeted implementations (pqac-00000007, pqac-00000010) | Hu et al. 2014, https://doi.org/10.1073/pnas.1410761111 (pqac-00000001, pqac-00000011); Kumar et al. 2022, https://doi.org/10.3389/fpls.2022.871890 (pqac-00000004); Yin et al. 2024, https://doi.org/10.3390/plants13192700 (pqac-00000007); Qiao et al. 2024, https://doi.org/10.3390/agronomy15010094 (pqac-00000010) |


*Table: This table summarizes identity, function, pathway context, and key quantitative findings for rice OsMET1a/MET1A using only evidence retrieved in the conversation. It separates direct experimental support from broader pathway-level inferences to aid careful functional annotation.*