MET-2 is the principal H3K9 mono- and dimethyltransferase in C. elegans, homologous to mammalian SETDB1. It catalyzes the sequential addition of one or two methyl groups to lysine 9 of histone H3 using S-adenosyl-L-methionine as the methyl donor, producing H3K9me1 and H3K9me2. MET-2-mediated H3K9 methylation is essential for heterochromatin formation, perinuclear chromatin anchoring, and transcriptional silencing of repetitive elements and developmental genes. The protein functions in a complex with LIN-65 (an ATF7IP homolog that mediates nuclear import and focus formation) and ARLE-14 (which stabilizes chromatin association). MET-2 has both catalytic and noncatalytic roles in gene silencing; even catalytically inactive MET-2 can form foci and maintain some repression by constraining histone acetylation. The enzyme primes chromatin for SET-25-mediated H3K9 trimethylation and is required for multiple developmental processes including vulval cell fate specification, meiotic sex chromosome inactivation, and transgenerational epigenetic inheritance.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0010629 negative regulation of gene expression | IBA GO_REF:0000033 | ACCEPT | Summary: MET-2 negatively regulates gene expression through H3K9 methylation-mediated heterochromatin formation. Multiple studies demonstrate that MET-2 represses transcription of lin-3 EGF (PMID:17634190), genes on the X chromosome during MSCI (PMID:21909284), and subtype-specific neuronal genes (PMID:24348272). The IBA annotation based on phylogenetic inference is well-supported by experimental evidence. Reason: This annotation accurately captures a core function of MET-2. As an H3K9 methyltransferase, MET-2 deposits repressive chromatin marks that silence gene expression. This is supported by multiple experimental studies in C. elegans. Supporting Evidence: PMID:17634190 met-2 is homologous to human SETDB1, an H3K9 HMT that represses transcription PMID:24348272 loss of cec-3, met-1, met-2 and lin-13, like loss of pqe-1... suggesting these genes act together to inhibit transcription |
| GO:0046974 histone H3K9 methyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: MET-2 is established as the principal H3K9 mono- and dimethyltransferase in C. elegans. Towbin et al. (PMID:22939621) demonstrated that "MET-2, a SETDB1 homolog, mediates mono- and dimethylation" of H3K9. This core enzymatic activity is conserved from the SETDB1 family. Reason: This is the core molecular function of MET-2. The IBA annotation is strongly supported by experimental evidence demonstrating H3K9 methyltransferase activity in vivo. Supporting Evidence: PMID:22939621 MET-2, a SETDB1 homolog, mediates mono- and dimethylation file:worm/met-2/met-2-uniprot.txt Histone methyltransferase which is required for the mono- and dimethylation of 'Lys-9' of histone H3 |
| GO:0070828 heterochromatin organization | IBA GO_REF:0000033 | ACCEPT | Summary: MET-2 is essential for heterochromatin organization in C. elegans. The protein forms nuclear foci that colocalize with H3K9me2 at the nuclear periphery. MET-2-dependent H3K9me2 is required for perinuclear anchoring of heterochromatin domains. Delaney et al. (2019) showed that met-2 mutants abolish peripheral enrichment of autosomal arms. Reason: Heterochromatin organization is a core biological process for MET-2. The H3K9me2 mark deposited by MET-2 is specifically required for nuclear lamina association and proper heterochromatin architecture. Supporting Evidence: PMID:22939621 elimination of two HMTs, MET-2 and SET-25, mimics the loss of SAM synthetase, abrogating the perinuclear attachment of heterochromatic transgenes file:worm/met-2/met-2-deep-research-falcon.md met-2 mutants abolish peripheral enrichment of autosomal arms measured by LEM-2 ChIP-seq |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: MET-2 localizes to the nucleus where it forms subnuclear foci enriched at the nuclear periphery. Nuclear localization is regulated and developmentally timed, with MET-2 accumulating in nuclear hubs at gastrulation (PMID:22939621, Mutlu et al. 2018). Reason: Nuclear localization is essential for MET-2's chromatin-modifying function. Multiple studies confirm nuclear localization with experimental evidence. Supporting Evidence: file:worm/met-2/met-2-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621} file:worm/met-2/met-2-deep-research-falcon.md nuclear MET-2 accumulation correlates with linear H3K9me2 increase |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This annotation is inferred from the MBD (methyl-CpG-binding domain) present in MET-2. However, MET-2's primary substrate is histone H3, not DNA directly. While the MBD domain may contribute to chromatin targeting, there is no direct experimental evidence for sequence-specific DNA binding activity. Reason: The IEA annotation based on InterPro MBD domain is technically accurate as MET-2 contains an MBD domain (IPR001739), but DNA binding is not the primary or core function. MET-2 functions as a histone methyltransferase and its chromatin targeting involves protein-protein interactions with LIN-65 and ARLE-14 rather than direct DNA binding. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: This IEA annotation for nuclear localization is consistent with experimental evidence. MET-2 is a nuclear protein that forms foci at the nuclear periphery. Reason: Redundant with the IBA annotation but correctly captures nuclear localization, which is experimentally validated. Supporting Evidence: file:worm/met-2/met-2-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621} |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: MET-2 associates with chromatin/chromosomes to deposit H3K9 methylation marks. The UniProt subcellular location indicates chromosome association, which is consistent with its function as a histone-modifying enzyme. Reason: Chromosome localization is expected for a histone methyltransferase and is supported by functional evidence showing MET-2 modifies chromatin-associated histones. Supporting Evidence: file:worm/met-2/met-2-uniprot.txt SUBCELLULAR LOCATION: Nucleus... Chromosome {ECO:0000305|PubMed:22939621} |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: MET-2 is found in both cytoplasm and nucleus, with regulated nuclear accumulation during development. In early embryos, MET-2 is predominantly cytoplasmic before translocating to the nucleus at gastrulation. Reason: Cytoplasmic localization is experimentally validated. MET-2's regulated nucleocytoplasmic distribution is an important aspect of its developmental regulation. Supporting Evidence: file:worm/met-2/met-2-uniprot.txt SUBCELLULAR LOCATION: Nucleus... Cytoplasm {ECO:0000269|PubMed:22939621} file:worm/met-2/met-2-deep-research-falcon.md MET-2/LIN-65/ARLE-14 move from cytosol to nuclear hubs with development |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000043 | MODIFY | Summary: This annotation is too general and does not accurately capture MET-2's role. MET-2 does not directly participate in transcription; rather, it represses transcription through chromatin modification. Reason: MET-2 is a negative regulator of transcription through heterochromatin formation, not a transcription factor or component of the transcription machinery. The annotation should be more specific about the regulatory role. Proposed replacements: negative regulation of gene expression |
| GO:0007548 sex differentiation | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: MET-2 plays a role in meiotic sex chromosome inactivation (MSCI) in males. Checchi & Engebrecht (PMID:21909284) showed that MET-2 mediates the transcriptional silencing program of meiotic sex chromosome inactivation. However, this is not a core function of MET-2. Reason: While MET-2 does function in sex-related processes (MSCI), this represents a context-specific application of its general heterochromatin-forming activity rather than a core function. Supporting Evidence: PMID:21909284 MET-2 also mediates the transcriptional silencing program of meiotic sex chromosome inactivation (MSCI) |
| GO:0008168 methyltransferase activity | IEA GO_REF:0000043 | MODIFY | Summary: MET-2 is indeed a methyltransferase, but this term is too general. The specific activity is histone H3K9 methyltransferase activity (GO:0046974). Reason: While accurate, this general term should be replaced with the more specific H3K9 methyltransferase activity annotation that better describes MET-2's enzymatic function. Proposed replacements: histone H3K9 methyltransferase activity |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: MET-2's pre-SET domain binds zinc ions in a triangular cluster arrangement. The UniProt entry documents multiple zinc binding sites in the pre-SET and post-SET domains (positions 973, 975, 979, 985, 987, 1030, 1034, 1036, 1041, 1237, 1290, 1292, 1297). Reason: Zinc binding is structurally important for SET domain-containing methyltransferases and is well-documented for MET-2 based on domain architecture. Supporting Evidence: file:worm/met-2/met-2-uniprot.txt In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | MODIFY | Summary: This is a very general parent term. MET-2 does have transferase activity as it transfers methyl groups, but more specific terms are available. Reason: Too general. Should be annotated with the specific histone methyltransferase activity terms. Proposed replacements: histone H3K9 methyltransferase activity |
| GO:0030154 cell differentiation | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: MET-2 does play roles in developmental processes including vulval cell fate specification and neuronal differentiation. However, this is a broad term that encompasses many specific processes. Reason: While MET-2 does function in cell differentiation contexts (vulval cells, neurons), these are downstream consequences of its core heterochromatin-forming function rather than direct involvement in differentiation machinery. |
| GO:0032259 methylation | IEA GO_REF:0000043 | ACCEPT | Summary: MET-2 catalyzes histone methylation, specifically H3K9 mono- and dimethylation. This general biological process term is accurate but lacks specificity. Reason: Accurate but general. This term captures the biochemical process but more specific annotations (histone H3K9 methyltransferase activity) better describe the function. |
| GO:0042054 histone methyltransferase activity | IEA GO_REF:0000002 | ACCEPT | Summary: MET-2 is a histone methyltransferase. The annotation is correct but the more specific term GO:0046974 (histone H3K9 methyltransferase activity) should be preferred. Reason: Accurate annotation based on domain architecture. MET-2 contains SET, pre-SET, and post-SET domains characteristic of histone methyltransferases. Supporting Evidence: file:worm/met-2/met-2-uniprot.txt Histone methyltransferase which is required for the mono- and dimethylation of 'Lys-9' of histone H3 |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: MET-2 binds zinc ions through its pre-SET and post-SET domains. This general term is accurate but the more specific zinc ion binding (GO:0008270) is preferred. Reason: Accurate but general. Zinc binding is documented and functionally relevant for the SET domain architecture. |
| GO:0046974 histone H3K9 methyltransferase activity | IEA GO_REF:0000117 | ACCEPT | Summary: MET-2 catalyzes H3K9 mono- and dimethylation. This is the core molecular function and is well-supported by experimental evidence. Reason: Core molecular function annotation. Redundant with IBA and IMP annotations but correctly captures the enzymatic activity. Supporting Evidence: PMID:22939621 MET-2, a SETDB1 homolog, mediates mono- and dimethylation |
| GO:0051321 meiotic cell cycle | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: MET-2 functions in meiosis, particularly in meiotic sex chromosome inactivation and checkpoint regulation. PMID:21909284 shows MET-2 shields the male X chromosome from checkpoint machinery and mediates MSCI. Reason: While MET-2 does function during meiosis, this represents a specific developmental context for its general heterochromatin function rather than direct involvement in cell cycle progression. Supporting Evidence: PMID:21909284 MET-2 shields the male X chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation |
| GO:0140948 histone H3K9 monomethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: MET-2 specifically catalyzes H3K9 monomethylation as the first step in sequential H3K9 methylation. This is a core enzymatic activity supported by PMID:22939621. Reason: This specific molecular function is well-documented. MET-2 catalyzes the first step (H3K9me0 to H3K9me1) of the H3K9 methylation pathway. Supporting Evidence: PMID:22939621 MET-2, a SETDB1 homolog, mediates mono- and dimethylation file:worm/met-2/met-2-uniprot.txt Histone methyltransferase which is required for the mono- and dimethylation of 'Lys-9' of histone H3 |
| GO:0005634 nucleus | IC PMID:17634190 Two C. elegans histone methyltransferases repress lin-3 EGF ... | ACCEPT | Summary: Nuclear localization inferred by curator from the gene's function in transcriptional repression via histone modification. Reason: Correct annotation. Nuclear localization is experimentally validated in multiple studies. Supporting Evidence: PMID:17634190 met-2 is homologous to human SETDB1, an H3K9 HMT that represses transcription file:worm/met-2/met-2-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621} |
| GO:0046974 histone H3K9 methyltransferase activity | IMP PMID:17634190 Two C. elegans histone methyltransferases repress lin-3 EGF ... | ACCEPT | Summary: Andersen & Horvitz demonstrated that met-1 and met-2 mutant embryos had reduced H3K9 trimethylation, indicating MET-2 contributes to H3K9 methylation. While this study focused on trimethylation phenotypes, later work (PMID:22939621) clarified that MET-2 specifically mediates mono- and dimethylation. Reason: Core molecular function with direct experimental support. The IMP evidence from mutant phenotypes supports H3K9 methyltransferase activity. Supporting Evidence: PMID:17634190 met-1 and met-2 (1) are each required for the normal trimethylation of both H3K9 and H3K36 |
| GO:0046975 histone H3K36 methyltransferase activity | IMP PMID:17634190 Two C. elegans histone methyltransferases repress lin-3 EGF ... | REMOVE | Summary: Andersen & Horvitz reported that met-2 mutants showed reduced H3K36 trimethylation. However, this is likely an indirect effect. MET-2 is homologous to SETDB1, which is an H3K9-specific methyltransferase. MET-1 (SET2 homolog) is the direct H3K36 methyltransferase. The observed H3K36me3 reduction in met-2 mutants may reflect crosstalk between these marks or indirect effects on MET-1 activity. Reason: This annotation is likely incorrect based on evolutionary conservation and biochemical specificity. SETDB1-family proteins are H3K9-specific methyltransferases. The observed H3K36me3 phenotype in met-2 mutants is more likely an indirect consequence of H3K9me loss affecting H3K36 methylation machinery, not direct catalytic activity on H3K36. UniProt catalytic activity annotations (EC 2.1.1.367) specify H3K9 as the substrate. Supporting Evidence: PMID:17634190 met-1 and met-2 (1) are each required for the normal trimethylation of both H3K9 and H3K36 |
| GO:0010629 negative regulation of gene expression | IMP PMID:24348272 Histone methylation restrains the expression of subtype-spec... | ACCEPT | Summary: Uchida et al. showed that met-2 mutants derepress unc-4 expression in vulval VC neurons. "Endogenous unc-4 transcripts accumulate in all six VC neurons in pqe-1, cec-3, and met-2 mutants" - demonstrating MET-2's role in silencing subtype-specific gene expression. Reason: Core biological process with direct experimental evidence. Loss of met-2 leads to ectopic gene expression, demonstrating negative regulation of gene expression. Supporting Evidence: PMID:24348272 Endogenous unc-4 transcripts accumulate in all six VC neurons in pqe-1, cec-3, and met-2 mutants PMID:24348272 MET-2 is the C. elegans homolog of human SETDB1 |
| GO:0040029 epigenetic regulation of gene expression | IMP PMID:24979765 SPR-5 and MET-2 function cooperatively to reestablish an epi... | ACCEPT | Summary: Kerr et al. demonstrated that MET-2 functions in transgenerational epigenetic reprogramming with SPR-5. SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line. spr-5;met-2 double mutants show transgenerational sterility and heritable epigenetic defects. Reason: Core biological process demonstrating MET-2's role in epigenetic inheritance and germline reprogramming. This is a key function supported by strong experimental evidence. Supporting Evidence: PMID:24979765 SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line |
| GO:0005737 cytoplasm | IDA PMID:22939621 Step-wise methylation of histone H3K9 positions heterochroma... | ACCEPT | Summary: Towbin et al. demonstrated cytoplasmic localization of MET-2, particularly in early embryos before nuclear accumulation. The regulated nucleocytoplasmic distribution is an important aspect of developmental timing of heterochromatin formation. Reason: Direct experimental evidence (IDA) for cytoplasmic localization. MET-2's regulated nuclear import is key to timing heterochromatin establishment. Supporting Evidence: PMID:22939621 The two HMTs target H3K9 in a consecutive fashion: MET-2, a SETDB1 homolog, mediates mono- and dimethylation file:worm/met-2/met-2-uniprot.txt SUBCELLULAR LOCATION: Nucleus... Cytoplasm {ECO:0000269|PubMed:22939621} file:worm/met-2/met-2-deep-research-falcon.md MET-2/LIN-65/ARLE-14 move from cytosol to nuclear hubs with development |
| GO:0045835 negative regulation of meiotic nuclear division | IMP PMID:21909284 Caenorhabditis elegans histone methyltransferase MET-2 shiel... | KEEP AS NON CORE | Summary: Checchi & Engebrecht showed that MET-2 shields the male X chromosome from checkpoint machinery. Loss of met-2 leads to increased apoptosis through activation of the recombination checkpoint in X0 germ lines. However, MET-2 does not directly regulate meiotic division; rather, it prevents checkpoint-induced cell death. Reason: This represents a specific context-dependent phenotype rather than a direct role in regulating meiotic nuclear division. MET-2's function here is to silence the X chromosome to prevent inappropriate checkpoint activation, not to directly regulate meiosis. Supporting Evidence: PMID:21909284 Absence of met-2 in X0 germ lines results in increased apoptosis by activating the recombination checkpoint PMID:21909284 Absence of MET-2 triggers the recombination checkpoint in worms with a single X |
| GO:0072325 vulval cell fate commitment | IMP PMID:21437264 H3K9me2/3 binding of the MBT domain protein LIN-61 is essent... | KEEP AS NON CORE | Summary: Koester-Eiserfunke & Fischle demonstrated that MET-2 functions in vulval cell fate determination through H3K9 methylation. LIN-61 acts with HPL-2 and MET-2 in this pathway. Double mutants between lin-61 and met-2 show enhanced vulval defects. Reason: Vulval development is a well-studied context for MET-2 function, but this is a tissue-specific manifestation of the general gene silencing function rather than a core function of the protein. Supporting Evidence: PMID:21437264 establish interplay of the H3K9me2/3 binding proteins, LIN-61 and HPL-2, as well as the H3K9MT MET-2 in distinct developmental pathways PMID:17634190 identified met-1 and met-2 as negative regulators of vulval cell-fate specification |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IGI PMID:17634190 Two C. elegans histone methyltransferases repress lin-3 EGF ... | ACCEPT | Summary: Andersen & Horvitz showed that MET-2 represses lin-3 EGF transcription. Genetic interactions demonstrate that met-1 and met-2 act redundantly with HP1 homologs to repress transcription. Reason: Direct evidence for transcriptional repression function. This is more specific than the general "negative regulation of gene expression" and captures the mechanism of action. Supporting Evidence: PMID:17634190 repress transcription of the EGF gene lin-3, which encodes the signal that induces vulval development |
| GO:0040027 negative regulation of vulval development | IGI PMID:17634190 Two C. elegans histone methyltransferases repress lin-3 EGF ... | KEEP AS NON CORE | Summary: MET-2 negatively regulates vulval development by repressing lin-3 EGF expression. Genetic interactions with HP1 homologs and NuRD complex components support this role. Reason: While experimentally validated with strong genetic evidence, vulval development regulation is a tissue-specific phenotype resulting from MET-2's general function in transcriptional repression rather than a core function. Supporting Evidence: PMID:17634190 identified met-1 and met-2 as negative regulators of vulval cell-fate specification PMID:17634190 repress transcription of the EGF gene lin-3, which encodes the signal that induces vulval development |
| GO:0140942 histone H3K9 dimethyltransferase activity | IMP PMID:22939621 Step-wise methylation of histone H3K9 positions heterochroma... | NEW | Summary: MET-2 catalyzes the conversion of H3K9me1 to H3K9me2. Towbin et al. demonstrated that "MET-2, a SETDB1 homolog, mediates mono- and dimethylation" of H3K9. Reason: This specific enzymatic activity is a core molecular function of MET-2 and should be annotated. H3K9 dimethyltransferase activity (GO:0140942) specifically captures the me1-to-me2 conversion that MET-2 catalyzes. Supporting Evidence: PMID:22939621 MET-2, a SETDB1 homolog, mediates mono- and dimethylation file:worm/met-2/met-2-deep-research-falcon.md approximately 10-fold H3K9me2 increase between 20-50 and 51-100 cell stages |
| GO:0140719 constitutive heterochromatin formation | IMP PMID:22939621 Step-wise methylation of histone H3K9 positions heterochroma... | NEW | Summary: MET-2 is essential for constitutive heterochromatin formation through H3K9me2 deposition. This mark is characteristic of constitutive heterochromatin in metazoa. Reason: Constitutive heterochromatin formation is more specific than "heterochromatin organization" and better captures MET-2's role in establishing stable, refractory chromatin domains at repeats and the nuclear periphery. Supporting Evidence: PMID:22939621 elimination of two HMTs, MET-2 and SET-25, mimics the loss of SAM synthetase, abrogating the perinuclear attachment of heterochromatic transgenes file:worm/met-2/met-2-deep-research-falcon.md MET-2/H3K9me2 is essential for perinuclear anchoring of autosomal arms |
| GO:0010526 transposable element silencing | IMP PMID:27668659 Histone H3K9 methylation is dispensable for Caenorhabditis e... | NEW | Summary: MET-2 and SET-25 together protect repeat-rich genomic regions including transposable elements by suppressing transcription-induced replication stress through H3K9 methylation. Reason: Transposon silencing is a key function of H3K9 methyltransferases and represents a core biological process for MET-2. The UniProt function annotation specifically mentions this role. Supporting Evidence: PMID:27668659 H3K9me2 or H3K9me3 stabilizes and protects repeat-rich genomes by suppressing transcription-induced replication stress file:worm/met-2/met-2-deep-research-falcon.md loss destabilizes nuclear MET-2, lowers H3K9me2, disperses foci, and derepresses repeats |
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Download this section (compressed HTML)Q: Is MET-2 H3K9me1 activity truly sequential (me0->me1 then me1->me2) or can it add two methyl groups processively?
Q: What targets MET-2 to specific genomic loci - is it small RNA-dependent targeting via NRDE-3?
Q: Does MET-2 have any non-histone substrates?
Q: What is the molecular basis for the noncatalytic silencing function of MET-2?
Experiment: In vitro methyltransferase assay with recombinant MET-2 to confirm H3K9me1 and H3K9me2 product formation
Experiment: ChIP-seq for MET-2 compared to H3K9me2 to identify direct genomic targets
Experiment: Structural studies of MET-2-LIN-65-ARLE-14 complex
Experiment: Identify MET-2 interacting proteins by IP-MS in embryos at different developmental stages
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