Existing Annotations Review

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

Core Functions

MET-2 is the principal H3K9 mono- and dimethyltransferase in C. elegans, homologous to mammalian SETDB1. It catalyzes sequential addition of methyl groups to H3K9 using SAM as methyl donor. This is supported by genetic evidence (met-2 mutants lose H3K9me2) and biochemical conservation with SETDB1 family proteins (PMID:22939621, PMID:20107519).

Molecular Function:

histone H3K9 methyltransferase activity

MET-2 catalyzes the first step of H3K9 methylation (me0 to me1). This activity primes chromatin for subsequent dimethylation by MET-2 and trimethylation by SET-25 (PMID:22939621).

Molecular Function:

histone H3K9 monomethyltransferase activity

MET-2 catalyzes H3K9me1 to H3K9me2 conversion. H3K9me2 is the primary mark responsible for perinuclear heterochromatin anchoring (Delaney et al. 2019).

Molecular Function:

histone H3K9 dimethyltransferase activity

Directly Involved In:

heterochromatin organization negative regulation of gene expression

Cellular Locations:

nucleus

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:17634190

Two C. elegans histone methyltransferases repress lin-3 EGF transcription to inhibit vulval development.

MET-2 is homologous to human SETDB1, an H3K9 HMT that represses transcription

"met-2 is homologous to human SETDB1, an H3K9 HMT that represses transcription"
met-1 and met-2 are each required for normal trimethylation of both H3K9 and H3K36

"met-1 and met-2 (1) are each required for the normal trimethylation of both H3K9 and H3K36"
met-1 and met-2 act redundantly with C. elegans HP1 homologs

"act redundantly with each other as well as with the C. elegans HP1 homologs"
MET-2 represses transcription of lin-3 EGF gene

"repress transcription of the EGF gene lin-3, which encodes the signal that induces vulval development"

PMID:20107519

Differential localization and independent acquisition of the H3K9me2 and H3K9me3 chromatin modifications in the Caenorhabditis elegans adult germ line.

MET-2 is required for H3K9 mono- and dimethylation

"MET-2 is required for adult germline H3K9me2 but not H3K9me3"

PMID:21437264

H3K9me2/3 binding of the MBT domain protein LIN-61 is essential for Caenorhabditis elegans vulva development.

LIN-61, HPL-2, and MET-2 function together in vulva development

"establish interplay of the H3K9me2/3 binding proteins, LIN-61 and HPL-2, as well as the H3K9MT MET-2 in distinct developmental pathways"
H3K9me2/3 interaction is central to vulval cell fate determination

"Interestingly, lin-61 genetically interacts with two other synMuvB genes, hpl-2, an HP1 homologous H3K9me2/3 binding factor, and met-2, a SETDB1 homologous H3K9 methyl transferase (H3K9MT), in determining C"

PMID:21909284

Caenorhabditis elegans histone methyltransferase MET-2 shields the male X chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation.

MET-2 mediates meiotic sex chromosome inactivation (MSCI)

"that MET-2 also mediates the transcriptional silencing program of meiotic sex chromosome inactivation"
MET-2 blocks checkpoint signaling on the partnerless male X chromosome

"Absence of MET-2 triggers the recombination checkpoint in worms with a single X"
Loss of met-2 causes increased apoptosis through checkpoint activation

"Absence of met-2 in X0 germ lines results in increased apoptosis by activating the recombination checkpoint"

PMID:22939621

Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery.

MET-2 mediates H3K9 mono- and dimethylation

"The two HMTs target H3K9 in a consecutive fashion: MET-2, a SETDB1 homolog, mediates mono- and dimethylation"
SET-25 mediates H3K9 trimethylation

"SET-25, a previously uncharacterized HMT, deposits H3K9me3"
MET-2 and SET-25 together position heterochromatin at nuclear periphery

"elimination of two HMTs, MET-2 and SET-25, mimics the loss of SAM synthetase, abrogating the perinuclear attachment of heterochromatic transgenes"
MET-2 is a SETDB1 homolog

"MET-2, a SETDB1 homolog, mediates mono- and dimethylation"

PMID:24348272

Histone methylation restrains the expression of subtype-specific genes during terminal neuronal differentiation in Caenorhabditis elegans.

MET-2 silences subtype-specific genes during neuronal differentiation

"MET-2 is the C. elegans homolog of human SETDB1 and Drosophila Eggless"
met-2 mutants show ectopic unc-4 expression in VC neurons

"Endogenous unc-4 transcripts accumulate in all six VC neurons in pqe-1, cec-3, and met-2 mutants"

PMID:24685137

A histone methylation network regulates transgenerational epigenetic memory in C. elegans.

MET-2 required for small-RNA-induced H3K9 methylation

"identified multiple chromatin-modifying factors, including H3K4me1/me2 and H3K9me3 methyltransferases"

PMID:24979765

SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line.

MET-2 functions with SPR-5 in germline epigenetic reprogramming

"SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state"
spr-5;met-2 double mutants have synergistic sterility

"spr-5;met-2 double mutants have a synergistic effect on sterility, H3K4me2, and spermatogenesis expression"
MET-2 contributes to transgenerational epigenetic inheritance

"mutants in the H3K9me2 methyltransferase, met-2, result in transgenerational epigenetic effects"

PMID:26365259

The Nrde pathway mediates small-RNA-directed histone H3 lysine 27 trimethylation in Caenorhabditis elegans.

MET-2 required for small-RNA-induced H3K9 methylation

"Whereas set-25 and met-2 are required for K9 methylation, mes-2 is required for K27 methylation"

PMID:27668659

Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability.

MET-2 and SET-25 together protect repeat-rich genomic regions

"In met-2 set-25 double mutants, which lack all H3K9 methylation (H3K9me), embryos differentiate normally"
H3K9 methylation suppresses transcription-induced replication stress

"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

Deep research summary for MET-2

MET-2 nuclear accumulation times heterochromatin onset
LIN-65 rate-limits MET-2 nuclear entry
ARLE-14 stabilizes MET-2 chromatin association
Approximately 10-fold H3K9me2 increase at gastrulation
MET-2 forms nuclear foci with LIN-65
met-2 mutants abolish perinuclear anchoring of autosomal arms
H3K9me2 (not me3) is required for lamina tethering
Catalytically inactive MET-2 still forms foci and maintains some gene silencing
Noncatalytic function involves constraining histone acetylation

Suggested Experiments

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

📚 Additional Documentation

Deep Research Falcon

(met-2-deep-research-falcon.md)

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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: P34544
Protein Description: RecName: Full=Histone-lysine N-methyltransferase met-2; EC=2.1.1.- {ECO:0000305|PubMed:22939621}; EC=2.1.1.367 {ECO:0000305|PubMed:22939621};
Gene Information: Name=met-2; ORFNames=R05D3.11;
Organism (full): Caenorhabditis elegans.
Protein Family: Belongs to the class V-like SAM-binding methyltransferase
Key Domains: DNA-bd_dom_sf. (IPR016177); Methyl_CpG_DNA-bd. (IPR001739); Post-SET_dom. (IPR003616); Pre-SET_dom. (IPR007728); SET_dom. (IPR001214)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "met-2" matches the protein description above
Verify the organism is correct: Caenorhabditis elegans.
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'met-2' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene met-2 (gene ID: met-2, UniProt: P34544) in worm.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: P34544
Protein Description: RecName: Full=Histone-lysine N-methyltransferase met-2; EC=2.1.1.- {ECO:0000305|PubMed:22939621}; EC=2.1.1.367 {ECO:0000305|PubMed:22939621};
Gene Information: Name=met-2; ORFNames=R05D3.11;
Organism (full): Caenorhabditis elegans.
Protein Family: Belongs to the class V-like SAM-binding methyltransferase
Key Domains: DNA-bd_dom_sf. (IPR016177); Methyl_CpG_DNA-bd. (IPR001739); Post-SET_dom. (IPR003616); Pre-SET_dom. (IPR007728); SET_dom. (IPR001214)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "met-2" matches the protein description above
Verify the organism is correct: Caenorhabditis elegans.
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Please provide a comprehensive research report on the gene met-2 (gene ID: met-2, UniProt: P34544) in worm.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Plan and verification
- Identity check: We confirm the target is C. elegans met-2 (UniProt P34544), encoding a SET domain class V-like SAM-dependent histone-lysine N-methyltransferase homologous to vertebrate SETDB1/SETDB2. Literature consistently assigns MET-2 as the principal H3K9 mono- and di-methyltransferase in C. elegans embryos; SET-25 catalyzes H3K9 trimethylation. Key cofactors LIN-65 (ATF7IP-like) and ARLE-14 (ARL14EP-like) modulate MET-2 localization and chromatin association. These features align with the UniProt family and domain annotations (Pre-SET/SET/Post-SET) and with conserved SETDB biology. We find no conflicting use of the symbol “met-2” that would suggest a different gene in C. elegans. (mutlu2018regulatednuclearaccumulation pages 1-2, padeken2022establishmentofh3k9methylated pages 2-3, jash2024chromatinorganizationduring pages 2-4, delaney2019heterochromaticfociand pages 8-10)

Comprehensive research report
1) Key concepts and definitions with current understanding
- Enzymatic identity and reaction: MET-2 is the C. elegans SETDB1-like histone methyltransferase that deposits H3K9me1 and H3K9me2 in vivo, using S-adenosyl-L-methionine as methyl donor. SET-25 performs most H3K9me3 deposition. This division of labor is supported by genetic and biochemical evidence in worms and is consistent with conserved SETDB1 functions in other animals. (jash2024chromatinorganizationduring pages 2-4, padeken2022establishmentofh3k9methylated pages 2-3)
• Jash & Csankovszki (2024, review; DNA 4(1):64–83; published Feb 2024) summarize that MET-2 deposits H3K9me1/2 and SET-25 deposits H3K9me3 in C. elegans embryos; they compile multiple primary studies supporting this model. URL: https://doi.org/10.3390/dna4010004 (jash2024chromatinorganizationduring pages 2-4)
• Padeken, Methot & Gasser (2022, review; Nat Rev Mol Cell Biol 23:623–640; May 2022) discuss conserved H3K9 HMT modules and note worm MET-2’s SETDB-like features and partners; SET-25 catalyzes H3K9me3 including de novo nucleation via small-RNA pathways. URL: https://doi.org/10.1038/s41580-022-00483-w (padeken2022establishmentofh3k9methylated pages 2-3)
- Substrate specificity: In embryos, H3K9me2 rises sharply at gastrulation with MET-2 nuclear accumulation; H3K9me1 rises modestly; H3K9me3 also increases but is largely SET-25–dependent downstream of MET-2 priming. Quantitation by Mutlu et al. shows ~10-fold H3K9me2 increase between ~20–50 and 51–100 cell stages, ~2-fold H3K9me1, and ~6-fold H3K9me3, linking MET-2 activity to heterochromatin onset. URL: https://doi.org/10.1126/sciadv.aat6224 (Aug 2018) (mutlu2018regulatednuclearaccumulation pages 1-2)
- Biological role: H3K9 methylation marks heterochromatin at repeats/transposons and lineage-restricted genes, promoting transcriptional silencing, nuclear lamina association, and normal development. MET-2-dependent H3K9me2 is crucial for perinuclear anchoring; SET-25-mediated H3K9me3 is not strictly required for lamina tethering. URL: https://doi.org/10.1083/jcb.201811038 (Mar 2019) (delaney2019heterochromaticfociand pages 8-10)

2) Recent developments and latest research (emphasis 2023–2024)
- Developmental timing via XOL-1→MET-2 axis (2024): Jash et al. (PLOS Genetics; Aug 15, 2024) show that the sex-determination factor XOL-1, although low in hermaphrodites, regulates embryonic developmental timing and dosage compensation by modulating MET-2. Loss of xol-1 causes increased MET-2 expression and altered H3K9me2/3 in 20–100 cell embryos; met-2;xol-1 double mutants partially or fully reverse several accelerated-development phenotypes and precocious DCC loading. URL: https://doi.org/10.1371/journal.pgen.1011238 (jash2024xol1regulatesdevelopmental pages 3-5, jash2024xol1regulatesdevelopmental pages 15-17)
• Quantitative highlights: H3K9me2/H3 levels significantly increase in xol-1 embryos at 20–50 cell (p=2.9×10−6) and 50–100 cell (p=4.2×10−14); H3K9me3 also increases (p=6.1×10−7 at 50–100 cells), and timing phenotypes (8-cell→bean, bean→2-fold transitions) are delayed toward WT when met-2 is removed in the xol-1 background. (jash2024xol1regulatesdevelopmental pages 15-17)
- H3K9me readers in lifespan/aging (2023): Hou et al. (Nature Communications; Mar 2023) systematically map chromodomain proteins and identify CEC-5 as an H3K9me1/2 reader whose chromatin association requires MET-2 and H3K9me1/2 at a substantial fraction of sites; both MET-2 and CEC-5 are required for normal lifespan. URL: https://doi.org/10.1038/s41467-023-36898-y (hou2023systematiccharacterizationof pages 8-11)
• Imaging/ChIP data show that met-2 mutation disrupts CEC-5 puncta and reduces CEC-5 binding at 779/3558 peaks enriched for H3K9me2; set-25 loss alone has minimal impact on these CEC-5 sites. (hou2023systematiccharacterizationof pages 8-11)
- Updated perspectives on embryonic chromatin organization (2024): Jash & Csankovszki review (Feb 2024) integrate MET-2’s nuclear hub formation with lamina tethering and the timing of heterochromatin onset; they emphasize LIN-65–mediated nuclear import and ARLE-14–mediated chromatin association, and note temperature/S-phase influences on MET-2 nuclear accumulation. URL: https://doi.org/10.3390/dna4010004 (jash2024chromatinorganizationduring pages 2-4)

3) Current applications and real-world implementations
- Temporal control of heterochromatin via MET-2 nuclear targeting: Mutlu et al. (2018) demonstrate that enforced nuclear accumulation of MET-2 leads to precocious H3K9 methylation and early heterochromatin domain formation, identifying a lever to time epigenome transitions during embryogenesis. URL: https://doi.org/10.1126/sciadv.aat6224 (mutlu2018regulatednuclearaccumulation pages 8-9, mutlu2018regulatednuclearaccumulation pages 1-2)
• Quantitative kinetics: nuclear MET-2 accumulation correlates with linear H3K9me2 increase; wild-type slopes vs arle-14 mutants show attenuated accumulation (e.g., 1–20 to 51–100 cells: slope ~0.41 WT vs ~0.15 arle-14), indicating ARLE-14’s role in chromatin engagement kinetics. (mutlu2018regulatednuclearaccumulation pages 8-9)
- Nuclear lamina/heterochromatin anchoring readouts: Delaney et al. (2019) use LEM-2 ChIP-seq, FISH, and reporters to show that met-2 loss abolishes peripheral association of autosomal arms whereas set-25 loss largely retains arm-periphery enrichment—implicating MET-2/H3K9me2 in perinuclear organization used as a cellular readout for heterochromatin integrity under stress or genetic perturbation. URL: https://doi.org/10.1083/jcb.201811038 (delaney2019heterochromaticfociand pages 8-10)
- Noncatalytic MET-2 function as a tool: Delaney et al. (2022) engineered a catalytically deficient MET-2 allele (C1237A; met-2-CD) that still forms LIN-65–dependent foci and partially maintains gene silencing and developmental fitness; this tool separates catalytic from structural roles for mechanistic dissection. URL: https://doi.org/10.1038/s41594-021-00712-4 (Jan 2022) (delaney2022setdb1likemet2promotes pages 4-5)
- Lifespan and chromodomain reporters: Hou et al. (2023) CRISPR-tagged chromodomain factors including CEC-5, enabling in vivo readouts of heterochromatin states sensitive to MET-2 and SUMOylation; platform applicable to aging and stress studies. URL: https://doi.org/10.1038/s41467-023-36898-y (hou2023systematiccharacterizationof pages 8-11)

4) Expert opinions and analysis from authoritative sources
- Conserved SETDB modules and reader/writer logic: Padeken et al. (2022) emphasize that MET-2 (worm SETDB1-like) associates with ATF7IP-like LIN-65 and ARLE-14, paralleling vertebrate SETDB1 with ATF7IP/KAP1/HP1. They highlight H3K9me1 as a priming state for SUV39-family H3K9me2/3 and the role of readers (HP1-like HPL-2; CEC-4/CEC-5) in chromatin compaction and nuclear architecture. URL: https://doi.org/10.1038/s41580-022-00483-w (padeken2022establishmentofh3k9methylated pages 2-3)
- Developmental timing of heterochromatin: Mutlu et al. (2018) provide a widely cited mechanistic framework: MET-2’s regulated nuclear accumulation establishes the onset of heterochromatin domains, with LIN-65 rate-limiting for nuclear entry and ARLE-14 stabilizing chromatin association. URL: https://doi.org/10.1126/sciadv.aat6224 (mutlu2018regulatednuclearaccumulation pages 1-2, mutlu2018regulatednuclearaccumulation pages 8-9)
- Nuclear lamina tethering: Delaney et al. (2019) argue MET-2/H3K9me2 is essential for perinuclear anchoring of autosomal arms, whereas H3K9me3 is dispensable for this specific architectural feature—refining the functional map of H3K9 states. URL: https://doi.org/10.1083/jcb.201811038 (delaney2019heterochromaticfociand pages 8-10)
- 2024 synthesis: Jash & Csankovszki (2024) incorporate new developmental regulators (e.g., XOL-1) and physiological variables (temperature, S-phase) into the MET-2 timing model, underscoring system-level control. URL: https://doi.org/10.3390/dna4010004 (jash2024chromatinorganizationduring pages 2-4)

5) Relevant statistics and data from recent and foundational studies
- H3K9 dynamics at gastrulation (Mutlu 2018, Sci Adv): ~10× increase in H3K9me2 (with MET-2 hubs), ~2× H3K9me1, ~6× H3K9me3 between ~20–50 and 51–100 cell stages; MET-2/LIN-65/ARLE-14 move from cytosol to nuclear hubs with development. URL: https://doi.org/10.1126/sciadv.aat6224 (mutlu2018regulatednuclearaccumulation pages 1-2)
- ARLE-14 effect sizes (Mutlu 2018): Early accumulation slopes of H3K9me2 are reduced in arle-14 mutants (e.g., 1–20→5–20 cells: ~0.11 WT vs ~0.02 arle-14; later 51–100 cells: ~0.41 WT vs ~0.15 arle-14), quantifying its role in MET-2 chromatin association. URL: https://doi.org/10.1126/sciadv.aat6224 (mutlu2018regulatednuclearaccumulation pages 8-9)
- Perinuclear tethering dependency (Delaney 2019, JCB): met-2 mutants abolish peripheral enrichment of autosomal arms measured by LEM-2 ChIP-seq and FISH; set-25 mutants retain arm-periphery enrichment, indicating H3K9me2 (not me3) is crucial for lamina association. URL: https://doi.org/10.1083/jcb.201811038 (delaney2019heterochromaticfociand pages 8-10)
- Noncatalytic MET-2 function (Delaney 2022, NSMB): met-2-CD reduces H3K9me2/3 to met-2Δ levels yet forms normal foci; met-2-CD animals show higher fertility than met-2Δ and maintain silencing at select loci by preventing H3K9/H3K27 acetylation increase. URLs: https://doi.org/10.1038/s41594-021-00712-4 (delaney2022setdb1likemet2promotes pages 4-5)
- XOL-1→MET-2 developmental timing (Jash 2024, PLOS Genet): xol-1 null elevates H3K9me2/3 in staged embryos (p-values: 2.9×10−6, 4.2×10−14 for H3K9me2; 6.1×10−7 for H3K9me3) and accelerates development; met-2 loss in xol-1 reverses accelerated transitions (8-cell→bean, bean→2-fold) and reduces precocious DCC loading categories. URL: https://doi.org/10.1371/journal.pgen.1011238 (jash2024xol1regulatesdevelopmental pages 3-5, jash2024xol1regulatesdevelopmental pages 15-17)
- H3K9me reader dependence and lifespan (Hou 2023, Nat Commun): CEC-5 puncta require MET-2; 779/3558 CEC-5 ChIP peaks reduced in met-2;set-25 double mutants and met-2 single mutants, but not set-25 alone; MET-2 and CEC-5 are both required for normal lifespan. URL: https://doi.org/10.1038/s41467-023-36898-y (hou2023systematiccharacterizationof pages 8-11)

Mechanistic synthesis: function, localization, partners, pathways
- Catalysis and pathway placement: MET-2 lays down H3K9me1/2 that primes and scaffolds heterochromatin formation, including recruitment/propagation of H3K9me3 by SET-25 at select loci (some via NRDE-3-dependent small RNA pathways). MET-2’s H3K9me2, more than H3K9me3, underpins lamina-associated domain (LAD) tethering in embryos. (jash2024chromatinorganizationduring pages 2-4, padeken2022establishmentofh3k9methylated pages 2-3, delaney2019heterochromaticfociand pages 8-10)
- Localization: Endogenous MET-2 is nuclear throughout development but concentrates into subnuclear hubs/foci at gastrulation; these foci are enriched at the periphery and co-localize with H3K9me2, while excluding active marks. Foci display stress-responsive dynamics (heat shock dispersal and recovery) paralleling LIN-65 behavior. (delaney2019heterochromaticfociand pages 8-10, mutlu2018regulatednuclearaccumulation pages 1-2)
- Cofactors: LIN-65 is ATF7IP-like, largely unstructured, and rate-limits MET-2 nuclear accumulation and focus formation; its loss destabilizes nuclear MET-2, lowers H3K9me2, disperses foci, and derepresses repeats and MET-2 targets. ARLE-14 enhances MET-2’s stable chromatin association and the kinetics of H3K9me2 accumulation; arle-14 mutants show delayed H3K9me2 accumulation with reduced slopes. (mutlu2018regulatednuclearaccumulation pages 8-9, mutlu2018regulatednuclearaccumulation pages 1-2, delaney2019heterochromaticfociand pages 8-10)
- Noncatalytic role: MET-2—via LIN-65–dependent foci—can repress specific genes and maintain fertility/fitness independently of H3K9 methyltransferase activity, in part by constraining histone acetylation (H3K9ac/H3K27ac). This separates structural/organizational functions from catalytic ones. (delaney2022setdb1likemet2promotes pages 4-5)
- Readers and aging: CEC-5 reads H3K9me1/2 in vitro and in vivo, requiring MET-2 for proper chromatin association and nuclear puncta; MET-2 and CEC-5 jointly support normal lifespan in C. elegans, linking MET-2’s marks to aging biology. (hou2023systematiccharacterizationof pages 8-11)
- Dosage compensation/sex determination: XOL-1 modulates MET-2 expression and thereby the H3K9 landscape and developmental timing in hermaphrodite embryos; MET-2 loss suppresses accelerated developmental phenotypes and precocious DCC loading in xol-1 mutants. (jash2024xol1regulatesdevelopmental pages 3-5, jash2024xol1regulatesdevelopmental pages 15-17)

Limitations and open questions
- How MET-2 is targeted to specific sequences (e.g., repeats vs developmental genes) remains an active area, likely involving small RNAs (NRDE-3) and readers like CEC proteins. The exact biochemical determinants of LIN-65/ARLE-14 interactions and whether MET-2–LIN-65 hubs are phase-separated condensates warrant further biophysical work. (jash2024chromatinorganizationduring pages 2-4, padeken2022establishmentofh3k9methylated pages 2-3, delaney2019heterochromaticfociand pages 8-10)

References with URLs and dates (selection)
- Mutlu et al., Science Advances, Aug 2018. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos. URL: https://doi.org/10.1126/sciadv.aat6224 (mutlu2018regulatednuclearaccumulation pages 8-9, mutlu2018regulatednuclearaccumulation pages 1-2, mutlu2018regulatednuclearaccumulation pages 14-14)
- Delaney et al., Journal of Cell Biology, Mar 2019. Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65. URL: https://doi.org/10.1083/jcb.201811038 (delaney2019heterochromaticfociand pages 8-10)
- Delaney et al., Nature Structural & Molecular Biology, Jan 2022. SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity. URL: https://doi.org/10.1038/s41594-021-00712-4 (delaney2022setdb1likemet2promotes pages 4-5)
- Padeken, Methot & Gasser, Nature Reviews Mol Cell Biol, May 2022. Establishment of H3K9-methylated heterochromatin… URL: https://doi.org/10.1038/s41580-022-00483-w (padeken2022establishmentofh3k9methylated pages 2-3)
- Hou et al., Nature Communications, Mar 2023. Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans. URL: https://doi.org/10.1038/s41467-023-36898-y (hou2023systematiccharacterizationof pages 8-11)
- Jash & Csankovszki, DNA, Feb 2024. Chromatin Organization during C. elegans Early Development. URL: https://doi.org/10.3390/dna4010004 (jash2024chromatinorganizationduring pages 2-4)
- Jash et al., PLOS Genetics, Aug 15, 2024. XOL-1 regulates developmental timing by modulating the H3K9 landscape in C. elegans early embryos. URL: https://doi.org/10.1371/journal.pgen.1011238 (jash2024xol1regulatesdevelopmental pages 3-5, jash2024xol1regulatesdevelopmental pages 15-17)

Conclusions
MET-2 (UniProt P34544) is the principal H3K9me1/2 writer in C. elegans that times heterochromatin establishment through regulated nuclear accumulation and formation of LIN-65/ARLE-14–dependent nuclear hubs. Its catalytic output (H3K9me2) is essential for lamina tethering and repression of repeats, while a distinct, LIN-65–dependent noncatalytic function helps maintain gene silencing and developmental fitness. In 2023–2024, work linked MET-2’s H3K9 landscape to developmental timing via XOL-1 and to lifespan via the H3K9me1/2 reader CEC-5, highlighting MET-2 as a central hub integrating gene regulation, nuclear architecture, development, and aging. (mutlu2018regulatednuclearaccumulation pages 1-2, delaney2019heterochromaticfociand pages 8-10, delaney2022setdb1likemet2promotes pages 4-5, hou2023systematiccharacterizationof pages 8-11, jash2024chromatinorganizationduring pages 2-4, jash2024xol1regulatesdevelopmental pages 3-5)

References

(mutlu2018regulatednuclearaccumulation pages 1-2): Beste Mutlu, Huei-Mei Chen, James J. Moresco, Barbara D. Orelo, Bing Yang, John M. Gaspar, Sabine Keppler-Ross, John R. Yates, David H. Hall, Eleanor M. Maine, and Susan E. Mango. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in c. elegans embryos. Science Advances, Aug 2018. URL: https://doi.org/10.1126/sciadv.aat6224, doi:10.1126/sciadv.aat6224. This article has 77 citations and is from a highest quality peer-reviewed journal.
(padeken2022establishmentofh3k9methylated pages 2-3): Jan Padeken, Stephen P. Methot, and Susan M. Gasser. Establishment of h3k9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nature Reviews. Molecular Cell Biology, 23:623-640, May 2022. URL: https://doi.org/10.1038/s41580-022-00483-w, doi:10.1038/s41580-022-00483-w. This article has 500 citations.
(jash2024chromatinorganizationduring pages 2-4): Eshna Jash and Györgyi Csankovszki. Chromatin organization during c. elegans early development. DNA, 4 1:64-83, Feb 2024. URL: https://doi.org/10.3390/dna4010004, doi:10.3390/dna4010004. This article has 7 citations.
(delaney2019heterochromaticfociand pages 8-10): Colin E. Delaney, Stephen P. Methot, Micol Guidi, Iskra Katic, Susan M. Gasser, and Jan Padeken. Heterochromatic foci and transcriptional repression by an unstructured met-2/setdb1 co-factor lin-65. The Journal of Cell Biology, 218:820-838, Mar 2019. URL: https://doi.org/10.1083/jcb.201811038, doi:10.1083/jcb.201811038. This article has 36 citations.
(jash2024xol1regulatesdevelopmental pages 3-5): Eshna Jash, Anati Alyaa Azhar, Hector Mendoza, Zoey M. Tan, Halle Nicole Escher, Dalia S. Kaufman, and Györgyi Csankovszki. Xol-1 regulates developmental timing by modulating the h3k9 landscape in c. elegans early embryos. PLOS Genetics, 20:e1011238, Aug 2024. URL: https://doi.org/10.1371/journal.pgen.1011238, doi:10.1371/journal.pgen.1011238. This article has 3 citations and is from a domain leading peer-reviewed journal.
(jash2024xol1regulatesdevelopmental pages 15-17): Eshna Jash, Anati Alyaa Azhar, Hector Mendoza, Zoey M. Tan, Halle Nicole Escher, Dalia S. Kaufman, and Györgyi Csankovszki. Xol-1 regulates developmental timing by modulating the h3k9 landscape in c. elegans early embryos. PLOS Genetics, 20:e1011238, Aug 2024. URL: https://doi.org/10.1371/journal.pgen.1011238, doi:10.1371/journal.pgen.1011238. This article has 3 citations and is from a domain leading peer-reviewed journal.
(hou2023systematiccharacterizationof pages 8-11): Xinhao Hou, Mingjing Xu, Chengming Zhu, Jianing Gao, Meili Li, Xiangyang Chen, Cheng Sun, Björn Nashan, Jianye Zang, Ying Zhou, Shouhong Guang, and Xuezhu Feng. Systematic characterization of chromodomain proteins reveals an h3k9me1/2 reader regulating aging in c. elegans. Nature Communications, Mar 2023. URL: https://doi.org/10.1038/s41467-023-36898-y, doi:10.1038/s41467-023-36898-y. This article has 13 citations and is from a highest quality peer-reviewed journal.
(mutlu2018regulatednuclearaccumulation pages 8-9): Beste Mutlu, Huei-Mei Chen, James J. Moresco, Barbara D. Orelo, Bing Yang, John M. Gaspar, Sabine Keppler-Ross, John R. Yates, David H. Hall, Eleanor M. Maine, and Susan E. Mango. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in c. elegans embryos. Science Advances, Aug 2018. URL: https://doi.org/10.1126/sciadv.aat6224, doi:10.1126/sciadv.aat6224. This article has 77 citations and is from a highest quality peer-reviewed journal.
(delaney2022setdb1likemet2promotes pages 4-5): Colin E. Delaney, Stephen P. Methot, Veronique Kalck, Jan Seebacher, Daniel Hess, Susan M. Gasser, and Jan Padeken. Setdb1-like met-2 promotes transcriptional silencing and development independently of its h3k9me-associated catalytic activity. Nature Structural & Molecular Biology, 29:85-96, Jan 2022. URL: https://doi.org/10.1038/s41594-021-00712-4, doi:10.1038/s41594-021-00712-4. This article has 26 citations and is from a highest quality peer-reviewed journal.
(mutlu2018regulatednuclearaccumulation pages 14-14): Beste Mutlu, Huei-Mei Chen, James J. Moresco, Barbara D. Orelo, Bing Yang, John M. Gaspar, Sabine Keppler-Ross, John R. Yates, David H. Hall, Eleanor M. Maine, and Susan E. Mango. Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in c. elegans embryos. Science Advances, Aug 2018. URL: https://doi.org/10.1126/sciadv.aat6224, doi:10.1126/sciadv.aat6224. This article has 77 citations and is from a highest quality peer-reviewed journal.

Citations

jash2024chromatinorganizationduring pages 2-4
mutlu2018regulatednuclearaccumulation pages 1-2
delaney2019heterochromaticfociand pages 8-10
hou2023systematiccharacterizationof pages 8-11
mutlu2018regulatednuclearaccumulation pages 8-9
mutlu2018regulatednuclearaccumulation pages 14-14
https://doi.org/10.3390/dna4010004
https://doi.org/10.1038/s41580-022-00483-w
https://doi.org/10.1126/sciadv.aat6224
https://doi.org/10.1083/jcb.201811038
https://doi.org/10.1371/journal.pgen.1011238
https://doi.org/10.1038/s41467-023-36898-y
https://doi.org/10.1038/s41594-021-00712-4
https://doi.org/10.1126/sciadv.aat6224,
https://doi.org/10.1038/s41580-022-00483-w,
https://doi.org/10.3390/dna4010004,
https://doi.org/10.1083/jcb.201811038,
https://doi.org/10.1371/journal.pgen.1011238,
https://doi.org/10.1038/s41467-023-36898-y,
https://doi.org/10.1038/s41594-021-00712-4,

📄 View Raw YAML

id: P34544
gene_symbol: met-2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: 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.
existing_annotations:
- term:
    id: GO:0010629
    label: negative regulation of gene expression
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:17634190
      supporting_text: met-2 is homologous to human SETDB1, an H3K9 HMT that represses
        transcription
    - reference_id: PMID:24348272
      supporting_text: loss of cec-3, met-1, met-2 and lin-13, like loss of pqe-1...
        suggesting these genes act together to inhibit transcription
- term:
    id: GO:0046974
    label: histone H3K9 methyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: MET-2, a SETDB1 homolog, mediates mono- and dimethylation
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: Histone methyltransferase which is required for the mono- and
        dimethylation of 'Lys-9' of histone H3
- term:
    id: GO:0070828
    label: heterochromatin organization
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: elimination of two HMTs, MET-2 and SET-25, mimics the loss
        of SAM synthetase, abrogating the perinuclear attachment of heterochromatic
        transgenes
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: met-2 mutants abolish peripheral enrichment of autosomal arms
        measured by LEM-2 ChIP-seq
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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).
    action: ACCEPT
    reason: Nuclear localization is essential for MET-2's chromatin-modifying function.
      Multiple studies confirm nuclear localization with experimental evidence.
    supported_by:
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621}'
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: nuclear MET-2 accumulation correlates with linear H3K9me2 increase
- term:
    id: GO:0003677
    label: DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: ACCEPT
    reason: Redundant with the IBA annotation but correctly captures nuclear localization,
      which is experimentally validated.
    supported_by:
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621}'
- term:
    id: GO:0005694
    label: chromosome
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    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.
    action: ACCEPT
    reason: Chromosome localization is expected for a histone methyltransferase and
      is supported by functional evidence showing MET-2 modifies chromatin-associated
      histones.
    supported_by:
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Nucleus... Chromosome {ECO:0000305|PubMed:22939621}'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    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.
    action: ACCEPT
    reason: Cytoplasmic localization is experimentally validated. MET-2's regulated
      nucleocytoplasmic distribution is an important aspect of its developmental regulation.
    supported_by:
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Nucleus... Cytoplasm {ECO:0000269|PubMed:22939621}'
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: MET-2/LIN-65/ARLE-14 move from cytosol to nuclear hubs with
        development
- term:
    id: GO:0006351
    label: DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0010629
      label: negative regulation of gene expression
- term:
    id: GO:0007548
    label: sex differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:21909284
      supporting_text: MET-2 also mediates the transcriptional silencing program of
        meiotic sex chromosome inactivation (MSCI)
- term:
    id: GO:0008168
    label: methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: MET-2 is indeed a methyltransferase, but this term is too general. The
      specific activity is histone H3K9 methyltransferase activity (GO:0046974).
    action: MODIFY
    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_replacement_terms:
    - id: GO:0046974
      label: histone H3K9 methyltransferase activity
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    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).
    action: ACCEPT
    reason: Zinc binding is structurally important for SET domain-containing methyltransferases
      and is well-documented for MET-2 based on domain architecture.
    supported_by:
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: In the pre-SET domain, Cys residues bind 3 zinc ions that are
        arranged in a triangular cluster
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: MODIFY
    reason: Too general. Should be annotated with the specific histone methyltransferase
      activity terms.
    proposed_replacement_terms:
    - id: GO:0046974
      label: histone H3K9 methyltransferase activity
- term:
    id: GO:0030154
    label: cell differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0032259
    label: methylation
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: MET-2 catalyzes histone methylation, specifically H3K9 mono- and dimethylation.
      This general biological process term is accurate but lacks specificity.
    action: ACCEPT
    reason: Accurate but general. This term captures the biochemical process but more
      specific annotations (histone H3K9 methyltransferase activity) better describe
      the function.
- term:
    id: GO:0042054
    label: histone methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    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.
    action: ACCEPT
    reason: Accurate annotation based on domain architecture. MET-2 contains SET,
      pre-SET, and post-SET domains characteristic of histone methyltransferases.
    supported_by:
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: Histone methyltransferase which is required for the mono- and
        dimethylation of 'Lys-9' of histone H3
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: ACCEPT
    reason: Accurate but general. Zinc binding is documented and functionally relevant
      for the SET domain architecture.
- term:
    id: GO:0046974
    label: histone H3K9 methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: MET-2 catalyzes H3K9 mono- and dimethylation. This is the core molecular
      function and is well-supported by experimental evidence.
    action: ACCEPT
    reason: Core molecular function annotation. Redundant with IBA and IMP annotations
      but correctly captures the enzymatic activity.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: MET-2, a SETDB1 homolog, mediates mono- and dimethylation
- term:
    id: GO:0051321
    label: meiotic cell cycle
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:21909284
      supporting_text: MET-2 shields the male X chromosome from checkpoint machinery
        and mediates meiotic sex chromosome inactivation
- term:
    id: GO:0140948
    label: histone H3K9 monomethyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: ACCEPT
    reason: This specific molecular function is well-documented. MET-2 catalyzes the
      first step (H3K9me0 to H3K9me1) of the H3K9 methylation pathway.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: MET-2, a SETDB1 homolog, mediates mono- and dimethylation
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: Histone methyltransferase which is required for the mono- and
        dimethylation of 'Lys-9' of histone H3
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IC
  original_reference_id: PMID:17634190
  review:
    summary: Nuclear localization inferred by curator from the gene's function in
      transcriptional repression via histone modification.
    action: ACCEPT
    reason: Correct annotation. Nuclear localization is experimentally validated in
      multiple studies.
    supported_by:
    - reference_id: PMID:17634190
      supporting_text: met-2 is homologous to human SETDB1, an H3K9 HMT that represses
        transcription
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621}'
- term:
    id: GO:0046974
    label: histone H3K9 methyltransferase activity
  evidence_type: IMP
  original_reference_id: PMID:17634190
  review:
    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.
    action: ACCEPT
    reason: Core molecular function with direct experimental support. The IMP evidence
      from mutant phenotypes supports H3K9 methyltransferase activity.
    supported_by:
    - reference_id: PMID:17634190
      supporting_text: met-1 and met-2 (1) are each required for the normal trimethylation
        of both H3K9 and H3K36
- term:
    id: GO:0046975
    label: histone H3K36 methyltransferase activity
  evidence_type: IMP
  original_reference_id: PMID:17634190
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:17634190
      supporting_text: met-1 and met-2 (1) are each required for the normal trimethylation
        of both H3K9 and H3K36
- term:
    id: GO:0010629
    label: negative regulation of gene expression
  evidence_type: IMP
  original_reference_id: PMID:24348272
  review:
    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.
    action: ACCEPT
    reason: Core biological process with direct experimental evidence. Loss of met-2
      leads to ectopic gene expression, demonstrating negative regulation of gene
      expression.
    supported_by:
    - reference_id: PMID:24348272
      supporting_text: Endogenous unc-4 transcripts accumulate in all six VC neurons
        in pqe-1, cec-3, and met-2 mutants
    - reference_id: PMID:24348272
      supporting_text: MET-2 is the C. elegans homolog of human SETDB1
- term:
    id: GO:0040029
    label: epigenetic regulation of gene expression
  evidence_type: IMP
  original_reference_id: PMID:24979765
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:24979765
      supporting_text: SPR-5 and MET-2 function cooperatively to reestablish an epigenetic
        ground state during passage through the germ line
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:22939621
  review:
    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.
    action: ACCEPT
    reason: Direct experimental evidence (IDA) for cytoplasmic localization. MET-2's
      regulated nuclear import is key to timing heterochromatin establishment.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: 'The two HMTs target H3K9 in a consecutive fashion: MET-2,
        a SETDB1 homolog, mediates mono- and dimethylation'
    - reference_id: file:worm/met-2/met-2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Nucleus... Cytoplasm {ECO:0000269|PubMed:22939621}'
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: MET-2/LIN-65/ARLE-14 move from cytosol to nuclear hubs with
        development
- term:
    id: GO:0045835
    label: negative regulation of meiotic nuclear division
  evidence_type: IMP
  original_reference_id: PMID:21909284
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:21909284
      supporting_text: Absence of met-2 in X0 germ lines results in increased apoptosis
        by activating the recombination checkpoint
    - reference_id: PMID:21909284
      supporting_text: Absence of MET-2 triggers the recombination checkpoint in worms
        with a single X
- term:
    id: GO:0072325
    label: vulval cell fate commitment
  evidence_type: IMP
  original_reference_id: PMID:21437264
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:21437264
      supporting_text: establish interplay of the H3K9me2/3 binding proteins, LIN-61
        and HPL-2, as well as the H3K9MT MET-2 in distinct developmental pathways
    - reference_id: PMID:17634190
      supporting_text: identified met-1 and met-2 as negative regulators of vulval
        cell-fate specification
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: IGI
  original_reference_id: PMID:17634190
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:17634190
      supporting_text: repress transcription of the EGF gene lin-3, which encodes
        the signal that induces vulval development
- term:
    id: GO:0040027
    label: negative regulation of vulval development
  evidence_type: IGI
  original_reference_id: PMID:17634190
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:17634190
      supporting_text: identified met-1 and met-2 as negative regulators of vulval
        cell-fate specification
    - reference_id: PMID:17634190
      supporting_text: repress transcription of the EGF gene lin-3, which encodes
        the signal that induces vulval development
- term:
    id: GO:0140942
    label: histone H3K9 dimethyltransferase activity
  evidence_type: IMP
  original_reference_id: PMID:22939621
  review:
    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.
    action: NEW
    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.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: MET-2, a SETDB1 homolog, mediates mono- and dimethylation
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: approximately 10-fold H3K9me2 increase between 20-50 and 51-100
        cell stages
- term:
    id: GO:0140719
    label: constitutive heterochromatin formation
  evidence_type: IMP
  original_reference_id: PMID:22939621
  review:
    summary: MET-2 is essential for constitutive heterochromatin formation through
      H3K9me2 deposition. This mark is characteristic of constitutive heterochromatin
      in metazoa.
    action: NEW
    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.
    supported_by:
    - reference_id: PMID:22939621
      supporting_text: elimination of two HMTs, MET-2 and SET-25, mimics the loss
        of SAM synthetase, abrogating the perinuclear attachment of heterochromatic
        transgenes
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: MET-2/H3K9me2 is essential for perinuclear anchoring of autosomal
        arms
- term:
    id: GO:0010526
    label: transposable element silencing
  evidence_type: IMP
  original_reference_id: PMID:27668659
  review:
    summary: MET-2 and SET-25 together protect repeat-rich genomic regions including
      transposable elements by suppressing transcription-induced replication stress
      through H3K9 methylation.
    action: NEW
    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.
    supported_by:
    - reference_id: PMID:27668659
      supporting_text: H3K9me2 or H3K9me3 stabilizes and protects repeat-rich genomes
        by suppressing transcription-induced replication stress
    - reference_id: file:worm/met-2/met-2-deep-research-falcon.md
      supporting_text: loss destabilizes nuclear MET-2, lowers H3K9me2, disperses
        foci, and derepresses repeats
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:17634190
  title: Two C. elegans histone methyltransferases repress lin-3 EGF transcription
    to inhibit vulval development.
  findings:
  - statement: MET-2 is homologous to human SETDB1, an H3K9 HMT that represses transcription
    supporting_text: met-2 is homologous to human SETDB1, an H3K9 HMT that represses
      transcription
  - statement: met-1 and met-2 are each required for normal trimethylation of both
      H3K9 and H3K36
    supporting_text: met-1 and met-2 (1) are each required for the normal trimethylation
      of both H3K9 and H3K36
  - statement: met-1 and met-2 act redundantly with C. elegans HP1 homologs
    supporting_text: act redundantly with each other as well as with the C. elegans
      HP1 homologs
  - statement: MET-2 represses transcription of lin-3 EGF gene
    supporting_text: repress transcription of the EGF gene lin-3, which encodes the
      signal that induces vulval development
- id: PMID:20107519
  title: Differential localization and independent acquisition of the H3K9me2 and
    H3K9me3 chromatin modifications in the Caenorhabditis elegans adult germ line.
  findings:
  - statement: MET-2 is required for H3K9 mono- and dimethylation
    supporting_text: MET-2 is required for adult germline H3K9me2 but not H3K9me3
- id: PMID:21437264
  title: H3K9me2/3 binding of the MBT domain protein LIN-61 is essential for Caenorhabditis
    elegans vulva development.
  findings:
  - statement: LIN-61, HPL-2, and MET-2 function together in vulva development
    supporting_text: establish interplay of the H3K9me2/3 binding proteins, LIN-61
      and HPL-2, as well as the H3K9MT MET-2 in distinct developmental pathways
  - statement: H3K9me2/3 interaction is central to vulval cell fate determination
    supporting_text: Interestingly, lin-61 genetically interacts with two other synMuvB
      genes, hpl-2, an HP1 homologous H3K9me2/3 binding factor, and met-2, a SETDB1
      homologous H3K9 methyl transferase (H3K9MT), in determining C
- id: PMID:21909284
  title: Caenorhabditis elegans histone methyltransferase MET-2 shields the male X
    chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation.
  findings:
  - statement: MET-2 mediates meiotic sex chromosome inactivation (MSCI)
    supporting_text: that MET-2 also mediates the transcriptional silencing program
      of meiotic sex chromosome inactivation
  - statement: MET-2 blocks checkpoint signaling on the partnerless male X chromosome
    supporting_text: Absence of MET-2 triggers the recombination checkpoint in worms
      with a single X
  - statement: Loss of met-2 causes increased apoptosis through checkpoint activation
    supporting_text: Absence of met-2 in X0 germ lines results in increased apoptosis
      by activating the recombination checkpoint
- id: PMID:22939621
  title: Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear
    periphery.
  findings:
  - statement: MET-2 mediates H3K9 mono- and dimethylation
    supporting_text: 'The two HMTs target H3K9 in a consecutive fashion: MET-2, a
      SETDB1 homolog, mediates mono- and dimethylation'
  - statement: SET-25 mediates H3K9 trimethylation
    supporting_text: SET-25, a previously uncharacterized HMT, deposits H3K9me3
  - statement: MET-2 and SET-25 together position heterochromatin at nuclear periphery
    supporting_text: elimination of two HMTs, MET-2 and SET-25, mimics the loss of
      SAM synthetase, abrogating the perinuclear attachment of heterochromatic transgenes
  - statement: MET-2 is a SETDB1 homolog
    supporting_text: MET-2, a SETDB1 homolog, mediates mono- and dimethylation
- id: PMID:24348272
  title: Histone methylation restrains the expression of subtype-specific genes during
    terminal neuronal differentiation in Caenorhabditis elegans.
  findings:
  - statement: MET-2 silences subtype-specific genes during neuronal differentiation
    supporting_text: MET-2 is the C. elegans homolog of human SETDB1 and Drosophila
      Eggless
  - statement: met-2 mutants show ectopic unc-4 expression in VC neurons
    supporting_text: Endogenous unc-4 transcripts accumulate in all six VC neurons
      in pqe-1, cec-3, and met-2 mutants
- id: PMID:24685137
  title: A histone methylation network regulates transgenerational epigenetic memory
    in C. elegans.
  findings:
  - statement: MET-2 required for small-RNA-induced H3K9 methylation
    supporting_text: identified multiple chromatin-modifying factors, including H3K4me1/me2
      and H3K9me3 methyltransferases
- id: PMID:24979765
  title: SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground
    state during passage through the germ line.
  findings:
  - statement: MET-2 functions with SPR-5 in germline epigenetic reprogramming
    supporting_text: SPR-5 and MET-2 function cooperatively to reestablish an epigenetic
      ground state
  - statement: spr-5;met-2 double mutants have synergistic sterility
    supporting_text: spr-5;met-2 double mutants have a synergistic effect on sterility,
      H3K4me2, and spermatogenesis expression
  - statement: MET-2 contributes to transgenerational epigenetic inheritance
    supporting_text: mutants in the H3K9me2 methyltransferase, met-2, result in transgenerational
      epigenetic effects
- id: PMID:26365259
  title: The Nrde pathway mediates small-RNA-directed histone H3 lysine 27 trimethylation
    in Caenorhabditis elegans.
  findings:
  - statement: MET-2 required for small-RNA-induced H3K9 methylation
    supporting_text: Whereas set-25 and met-2 are required for K9 methylation, mes-2
      is required for K27 methylation
- id: PMID:27668659
  title: Histone H3K9 methylation is dispensable for Caenorhabditis elegans development
    but suppresses RNA:DNA hybrid-associated repeat instability.
  findings:
  - statement: MET-2 and SET-25 together protect repeat-rich genomic regions
    supporting_text: In met-2 set-25 double mutants, which lack all H3K9 methylation
      (H3K9me), embryos differentiate normally
  - statement: H3K9 methylation suppresses transcription-induced replication stress
    supporting_text: H3K9me2 or H3K9me3 stabilizes and protects repeat-rich genomes
      by suppressing transcription-induced replication stress
- id: file:worm/met-2/met-2-deep-research-falcon.md
  title: Deep research summary for MET-2
  findings:
  - statement: MET-2 nuclear accumulation times heterochromatin onset
  - statement: LIN-65 rate-limits MET-2 nuclear entry
  - statement: ARLE-14 stabilizes MET-2 chromatin association
  - statement: Approximately 10-fold H3K9me2 increase at gastrulation
  - statement: MET-2 forms nuclear foci with LIN-65
  - statement: met-2 mutants abolish perinuclear anchoring of autosomal arms
  - statement: H3K9me2 (not me3) is required for lamina tethering
  - statement: Catalytically inactive MET-2 still forms foci and maintains some gene
      silencing
  - statement: Noncatalytic function involves constraining histone acetylation
core_functions:
- molecular_function:
    id: GO:0046974
    label: histone H3K9 methyltransferase activity
  description: MET-2 is the principal H3K9 mono- and dimethyltransferase in C. elegans,
    homologous to mammalian SETDB1. It catalyzes sequential addition of methyl groups
    to H3K9 using SAM as methyl donor. This is supported by genetic evidence (met-2
    mutants lose H3K9me2) and biochemical conservation with SETDB1 family proteins
    (PMID:22939621, PMID:20107519).
- molecular_function:
    id: GO:0140948
    label: histone H3K9 monomethyltransferase activity
  description: MET-2 catalyzes the first step of H3K9 methylation (me0 to me1). This
    activity primes chromatin for subsequent dimethylation by MET-2 and trimethylation
    by SET-25 (PMID:22939621).
- molecular_function:
    id: GO:0140942
    label: histone H3K9 dimethyltransferase activity
  description: MET-2 catalyzes H3K9me1 to H3K9me2 conversion. H3K9me2 is the primary
    mark responsible for perinuclear heterochromatin anchoring (Delaney et al. 2019).
  directly_involved_in:
  - id: GO:0070828
    label: heterochromatin organization
  - id: GO:0010629
    label: negative regulation of gene expression
  locations:
  - id: GO:0005634
    label: nucleus
proposed_new_terms: []
suggested_questions:
- question: Is MET-2 H3K9me1 activity truly sequential (me0->me1 then me1->me2) or
    can it add two methyl groups processively?
- question: What targets MET-2 to specific genomic loci - is it small RNA-dependent
    targeting via NRDE-3?
- question: Does MET-2 have any non-histone substrates?
- question: What is the molecular basis for the noncatalytic silencing function of
    MET-2?
suggested_experiments:
- description: In vitro methyltransferase assay with recombinant MET-2 to confirm
    H3K9me1 and H3K9me2 product formation
- description: ChIP-seq for MET-2 compared to H3K9me2 to identify direct genomic targets
- description: Structural studies of MET-2-LIN-65-ARLE-14 complex
- description: Identify MET-2 interacting proteins by IP-MS in embryos at different
    developmental stages
tags:
- caeel-upr-stress

met-2

Gene Description

Existing Annotations Review

Core Functions

MET-2 catalyzes the first step of H3K9 methylation (me0 to me1). This activity primes chromatin for subsequent dimethylation by MET-2 and trimethylation by SET-25 (PMID:22939621).

MET-2 catalyzes H3K9me1 to H3K9me2 conversion. H3K9me2 is the primary mark responsible for perinuclear heterochromatin anchoring (Delaney et al. 2019).

References

Suggested Questions for Experts

Suggested Experiments

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Deep Research Falcon

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Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

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Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

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