meg-4

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005515 protein binding	IPI PMID:12445390 Integrating interactome, phenome, and transcriptome mapping ...	MARK AS OVER ANNOTATED	Summary: High-throughput yeast two-hybrid screen identified interactions with atz-1 and klc-1. The PMID:12445390 publication describes an integrated interactome mapping approach for C. elegans germline proteins. While the interaction data is valid, the generic term "protein binding" does not provide functional insight for a scaffold protein whose core function is phase separation-mediated granule assembly. Reason: The protein binding annotation from high-throughput Y2H screening is technically correct but uninformative. MEG-4 functions as a scaffold protein for P granule assembly through phase separation, and its biologically relevant interactions (e.g., with MEG-3) involve molecular condensate scaffold activity. Generic "protein binding" does not capture this functional context. The specific interactors (atz-1, klc-1) from this screen have not been validated for functional relevance to P granule biology. Supporting Evidence: PMID:12445390 we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue
GO:0005515 protein binding	IPI PMID:14704431 A map of the interactome network of the metazoan C. elegans.	MARK AS OVER ANNOTATED	Summary: Large-scale worm interactome mapping study identified MEG-4 interaction with ikb-1. This is a high-throughput Y2H screen with independent co-affinity purification validation. Reason: While the Y2H interaction is experimentally supported, the generic "protein binding" term lacks functional specificity. MEG-4 is an IDP scaffold protein whose meaningful interactions involve condensate assembly. The interaction with ikb-1 (IKK binding protein) has not been shown to be relevant to MEG-4's core function in P granule biology. A more informative MF annotation would capture the molecular condensate scaffold activity. Supporting Evidence: PMID:14704431 more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens
GO:0005515 protein binding	IPI PMID:19123269 Empirically controlled mapping of the Caenorhabditis elegans...	MARK AS OVER ANNOTATED	Summary: Empirically controlled C. elegans interactome study (WI-2007) with quality control framework showing interaction data similar in quality to low-throughput literature-curated data. Reason: This annotation comes from a rigorous high-throughput Y2H study with empirical quality control. However, "protein binding" remains an uninformative term for MEG-4, whose function depends on its ability to scaffold molecular condensates through multivalent interactions mediated by its intrinsically disordered regions. The annotation does not capture the functional significance of MEG-4's protein interactions. Supporting Evidence: PMID:19123269 the resulting dataset (Worm Interactome 2007 or WI-2007) is similar in quality to low-throughput data curated from the literature
GO:0051640 organelle localization	IMP PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	ACCEPT	Summary: Wang et al. (2014) demonstrated that MEG proteins regulate P granule dynamics through phosphorylation-controlled phase separation. MEG-4 functions redundantly with MEG-3 in localizing P granules to the posterior of the embryo (PMID:25535836). Reason: This annotation accurately captures MEG-4's role in P granule localization. The Wang et al. study provides direct mutant phenotype evidence that MEG proteins are required for proper organelle localization: "MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility." P granule segregation to the posterior involves MEG-regulated condensation/dissolution dynamics controlled by MBK-2/DYRK kinase and PP2A phosphatase. Supporting Evidence: PMID:25535836 Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly file:worm/meg-4/meg-4-deep-research-falcon.md MEG-4 is maternally provided and associates with embryonic P granules from the 1-cell through ~100-cell stage, segregating with the P lineage.
GO:1903863 P granule assembly	IGI PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	ACCEPT	Summary: MEG-3 and MEG-4 are required together (genetic interaction) for proper P granule assembly. The Wang et al. study shows MEGs stabilize the condensed phase of P granules through regulated phase separation. Reason: This is a core annotation for MEG-4 function. The IGI evidence code is appropriate as meg-3 meg-4 double mutants show synergistic defects in P granule assembly not seen in single mutants. MEG proteins localize to a dynamic domain surrounding P granules and are direct regulators of granule condensation dynamics through their intrinsically disordered, serine-rich regions that undergo phosphorylation-dependent phase transitions. Supporting Evidence: PMID:25535836 GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule PMID:25535836 despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation file:worm/meg-4/meg-4-deep-research-falcon.md total P granules in meg-3 meg-4 zygotes are reduced to ~11% of wild-type. file:worm/meg-4/meg-4-deep-research-falcon.md MEG-3 and MEG-4 are reported as ~71% identical and functionally redundant in embryonic P granule assembly.
GO:0036093 germ cell proliferation	IGI PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	KEEP AS NON CORE	Summary: MEG proteins are required for germ cell viability and proliferation. The meg-1 meg-3 meg-4 triple mutant is 100% sterile, indicating MEGs contribute redundantly to germline function. Reason: While MEG-4 is involved in germ cell proliferation, this represents a downstream consequence of its primary function in P granule assembly rather than a direct mechanistic role in cell proliferation. The sterility phenotype of triple mutants reflects failed germline development due to defective P granule function. This is a valid annotation but should be considered non-core compared to the direct molecular function in granule assembly. Supporting Evidence: PMID:25535836 The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility file:worm/meg-4/meg-4-deep-research-falcon.md meg-1 meg-3 meg-4 animals are reported as 100% sterile, with larvae exhibiting <10 germ cells and failure of germ cell proliferation.
GO:0005515 protein binding	IPI PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	MODIFY	Summary: Wang et al. identified specific protein interactions for MEG-4 in the context of P granule biology, including interactions with MEG-3 and phosphoregulators MBK-2 and PP2A(PPTR-1/2). Reason: While the IPI evidence from PMID:25535836 is more functionally relevant than the high-throughput Y2H studies (demonstrating interactions with MEG-3 and kinase/phosphatase regulators), "protein binding" still fails to capture MEG-4's molecular function. MEG-4 functions as a scaffold for molecular condensate assembly through its intrinsically disordered regions. The term GO:0140693 "molecular condensate scaffold activity" would more accurately describe MEG-4's molecular function. Proposed replacements: molecular condensate scaffold activity Supporting Evidence: PMID:25535836 we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules PMID:25535836 We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-½) file:worm/meg-4/meg-4-deep-research-falcon.md MEG-4 is described as a large, serine/threonine-rich protein with extensive predicted disorder and low-complexity regions, consistent with roles as a condensate scaffold/regulator.
GO:0043186 P granule	IDA PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	ACCEPT	Summary: Direct experimental observation showing MEG-4 localizes to P granules. Wang et al. used GFP-tagged MEG proteins and lattice light sheet microscopy to demonstrate localization to a dynamic domain surrounding and penetrating P granules. Reason: This is a well-supported cellular component annotation. IDA evidence from imaging studies directly demonstrates MEG-4 localization to P granules. The study further characterizes MEG proteins as localizing to a dynamic peripheral domain of P granules that regulates condensate assembly/disassembly. Supporting Evidence: PMID:25535836 GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule file:worm/meg-4/meg-4-deep-research-falcon.md A study reports experimental tagging of MEG-4 using C-terminal 3×FLAG via CRISPR for localization, supporting that MEG-4 itself is present in embryonic germ plasm granules.
GO:0140693 molecular condensate scaffold activity	IDA PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	NEW	Summary: MEG-4 is an intrinsically disordered protein that functions as a scaffold for P granule condensate assembly. Wang et al. demonstrate that MEG proteins regulate granule dynamics through phase separation controlled by phosphorylation. Reason: This annotation captures MEG-4's core molecular function as a scaffold that promotes the assembly of molecular condensates (P granules) through phase separation. MEG-4's long N-terminal intrinsically disordered region with serine-rich, polar residue composition (as documented in UniProt features) is characteristic of condensate scaffold proteins. The Wang et al. study demonstrates that MEG proteins directly regulate P granule condensation/dissolution dynamics through phosphorylation-dependent phase transitions. Supporting Evidence: PMID:25535836 we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos PMID:25535836 Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly file:worm/meg-4/meg-4-deep-research-falcon.md MEG-4 is predicted to be largely disordered (~69% predicted disorder; 570/832 aa)
GO:0060293 germ plasm	IDA PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser...	NEW	Summary: MEG-4 is a germ plasm component that localizes to P granules in the posterior cytoplasm of early embryos. Reason: MEG-4 is explicitly described as a germ plasm component. The germ plasm is the specialized cytoplasm inherited by germline precursor cells, and P granules are the defining feature of C. elegans germ plasm. This cellular component annotation complements the P granule annotation by placing MEG-4 in the broader context of germline specification. Supporting Evidence: PMID:25535836 The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility file:worm/meg-4/meg-4-deep-research-falcon.md acts redundantly with its close paralog MEG-3 to drive cytoplasmic (embryonic) P granule assembly

Core Functions

MEG-4 functions as an intrinsically disordered scaffold protein that promotes P granule assembly through phase separation. Its long disordered N-terminal region with serine-rich, polar residue composition enables multivalent interactions required for condensate formation. This is MEG-4's primary molecular function.

Molecular Function:

molecular condensate scaffold activity

Directly Involved In:

P granule assembly

Cellular Locations:

P granule germ plasm

Supporting Evidence:

PMID:25535836
we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
PMID:25535836
Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly
file:worm/meg-4/meg-4-deep-research-falcon.md
acts **redundantly with its close paralog MEG-3** to drive **cytoplasmic (embryonic) P granule assembly**
file:worm/meg-4/meg-4-deep-research-falcon.md
MEG-4 is described as a large, serine/threonine-rich protein with extensive predicted disorder and low-complexity regions, consistent with roles as a condensate scaffold/regulator.

References

PMID:12445390

Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.

MEG-4 identified in germline-enriched Y2H interactome screen

"we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue"
Interactions detected with atz-1 and klc-1

"we find that essential proteins have a tendency to interact with each other"

PMID:14704431

A map of the interactome network of the metazoan C. elegans.

Large-scale Y2H interactome mapping

"more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens"
MEG-4 interaction with ikb-1 identified

"Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set"

PMID:19123269

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

High-confidence interactome data (WI-2007)

"the resulting dataset (Worm Interactome 2007 or WI-2007) is similar in quality to low-throughput data curated from the literature"
Quality control framework validates Y2H data quality

"Through a new quality control empirical framework"

PMID:25535836

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans.

MEG proteins (MEG-1, MEG-3, MEG-4) are IDPs that regulate P granule dynamics

"we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos"
MEGs are substrates of MBK-2/DYRK kinase and PP2A phosphatase

"We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-½)"
Phosphorylation promotes granule disassembly, dephosphorylation promotes assembly

"Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly"
GFP-MEG-3 localizes to dynamic domain surrounding P granules

"GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule"
MEG proteins function redundantly for fertility

"The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility"

file:worm/meg-4/meg-4-deep-research-falcon.md

Falcon deep research report on C. elegans meg-4 (Q9TZK8 / C36C9.1)

MEG-4 acts redundantly with its close paralog MEG-3 to drive cytoplasmic (embryonic) P granule assembly and to promote preferential germline inheritance/enrichment of maternal mRNAs during early embryogenesis.

"acts **redundantly with its close paralog MEG-3** to drive **cytoplasmic (embryonic) P granule assembly**"
MEG-4 is a large (832 aa), serine/threonine-rich, largely intrinsically disordered MEG-family protein (~69% predicted disorder, 570/832 aa) with low-complexity regions, consistent with a condensate scaffold/regulator role.

"MEG-4 is predicted to be largely disordered (**~69% predicted disorder; 570/832 aa**)"
MEG-3 and MEG-4 are approximately 71% identical and functionally redundant in embryonic P granule assembly.

"MEG-3 and MEG-4 are reported as **~71% identical** and functionally redundant in embryonic P granule assembly."
MEG-4 is maternally provided and associates with embryonic P granules / germ plasm from the 1-cell through ~100-cell stage, segregating with the P lineage; a CRISPR C-terminal 3xFLAG tag was used to localize MEG-4.

"MEG-4 is maternally provided and associates with embryonic P granules from the **1-cell through ~100-cell stage**, segregating with the P lineage."
In meg-3 meg-4 double mutant zygotes, granule formation is severely impaired; total P granules during first mitosis are reduced to ~11% of wild-type, and nos-2 mRNA segregates symmetrically rather than with the germline blastomere.

"total P granules in meg-3 meg-4 zygotes are reduced to **~11% of wild-type**."
Genetic epistasis places meg-3/meg-4 downstream of the kinase MBK-2/DYRK and PP2A regulatory subunits PPTR-1/2 in controlling the balance of P granule assembly and disassembly.

"Genetic epistasis places *meg-3/meg-4* downstream of the kinase **MBK-2/DYRK** and PP2A regulatory subunits **PPTR-1/2** for controlling P granule assembly/disassembly."
meg-3/4-dependent P granules contribute to preferential germline enrichment/inheritance of particular maternal mRNAs (e.g. nos-2).

"MEG-3/4-dependent P granules contribute to **preferential germline enrichment/inheritance** of particular maternal mRNAs."
meg-4 single mutants show only a slight reduction in P granule number; the meg-3 meg-4 double mutant has the strongest embryonic assembly defect, indicating redundancy with MEG-3 contributing the larger share.

"*meg-4* single mutants show **only a slight reduction** in P granule number in zygotes"
MEG-1/MEG-3/MEG-4 are required for cytoplasmic but not perinuclear P granule formation; perinuclear granules reappear later (L1/L4), indicating a stage-specific requirement.

"**meg-1, meg-3, and meg-4 are required for cytoplasmic but not perinuclear P granule formation**"
meg-1 meg-3 meg-4 triple mutants are 100% sterile with larvae showing <10 germ cells and failure of germ cell proliferation, indicating MEG proteins contribute redundantly to germline development.

"**meg-1 meg-3 meg-4** animals are reported as **100% sterile**, with larvae exhibiting **<10 germ cells** and failure of germ cell proliferation."
The peer-reviewed literature does not support the UniProt "J domain-containing protein" name for MEG-4; no source describes MEG-4 as an Hsp40/J-domain co-chaperone or reports J-domain-dependent activities.

"none of these sources describe MEG-4 as an Hsp40/J-domain co-chaperone or report J-domain-dependent activities"

Suggested Experiments

Experiment: In vitro phase separation assays with purified MEG-4 to characterize its intrinsic condensation properties

Hypothesis: MEG-4 can undergo liquid-liquid phase separation in vitro dependent on protein concentration and phosphorylation state

Type: biochemical reconstitution

Experiment: Phosphomimetic and phospho-null mutations in MEG-4 to map critical phosphorylation sites for granule dynamics

Hypothesis: Specific serine residues in MEG-4 are required for MBK-2-dependent regulation of P granule assembly

Type: mutagenesis

Experiment: CLIP-seq to identify direct RNA targets of MEG-4

Hypothesis: MEG-4 directly binds specific mRNA populations that are recruited to P granules

Type: RNA-protein interaction

Experiment: Cryo-ET of P granules in wild-type vs meg-4 mutants to characterize granule ultrastructure

Hypothesis: MEG-4 contributes to the non-homogeneous internal structure of P granules

Type: structural biology

Deep Research

Falcon

(meg-4-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 25 citations 2 artifacts 2026-05-30T17:56:01.119357

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000019 I have extracted the requested visual information from the document. **Figure 2 (Page 6): MEG Disorder Prediction** Panel A shows t (image/png)

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.

Research report: Functional annotation of C. elegans meg-4 (ORF C36C9.1; UniProt Q9TZK8)

Executive summary

meg-4 encodes MEG-4, a maternally provided germ-plasm protein that acts redundantly with its close paralog MEG-3 to drive cytoplasmic (embryonic) P granule assembly and to promote preferential inheritance/enrichment of maternal mRNAs in the germline blastomeres during early embryogenesis. The strongest evidence for MEG-4 function is genetic and cell biological: meg-3 meg-4 double mutants lose most cytoplasmic P granules in embryos, show symmetric segregation of typical P-granule mRNAs (e.g., nos-2), and have partially penetrant sterility, while later perinuclear granules can recover, indicating a stage-specific requirement. Regulation of MEG-dependent granule dynamics is genetically downstream of MBK-2/DYRK and PP2A (PPTR-1/2). No evidence in the retrieved peer-reviewed literature supports the UniProt label “J domain-containing protein” for MEG-4; instead, the primary literature describes MEG-4 as a serine-rich, largely intrinsically disordered MEG-family protein closely related to MEG-3. (wang2014regulationofrna pages 5-7, wang2014regulationofrna pages 7-9, wang2014regulationofrna pages 11-13, wang2014regulationofrna pages 15-16)

1) Key concepts and definitions (current understanding)

Germ plasm, P granules, and condensates

In C. elegans embryos, P granules are cytoplasmic ribonucleoprotein (RNP) condensates that segregate with the germline (P lineage). Their formation and dissolution exhibit hallmarks of phase-separated assemblies, with different subdomains/components showing distinct dynamics. MEG proteins are central regulators of these dynamics in embryos. (wang2014regulationofrna pages 11-13, wang2014regulationofrna pages 15-16)

MEG proteins (maternal-effect germline defective)

MEG proteins are maternally contributed factors required redundantly for normal germline development. In the best-cited primary study defining MEG-3/4 function, MEG-4 is described as a large, serine/threonine-rich protein with extensive predicted disorder and low-complexity regions, consistent with roles as a condensate scaffold/regulator. (wang2014regulationofrna pages 5-7, wang2014regulationofrna pages 15-16)

2) Gene/protein identity verification and domain architecture

Verified identity in the literature

The literature retrieved here consistently uses meg-4 = MEG-4 = C36C9.1 in C. elegans, in the context of embryonic P granule assembly and germline determinant regulation. This matches the user-provided gene name/ORF and organism. (wang2014regulationofrna pages 7-9, wang2014regulationofrna pages 11-13)

Domain/family features supported by the literature

Intrinsic disorder/low complexity: MEG-4 is predicted to be largely disordered (~69% predicted disorder; 570/832 aa), with low-complexity regions detectable under appropriate SEG parameters. (wang2014regulationofrna pages 5-7, wang2014regulationofrna media 088f36bf)

Paralogy to MEG-3: MEG-3 and MEG-4 are reported as ~71% identical and functionally redundant in embryonic P granule assembly. (wang2014regulationofrna pages 5-7, wang2014regulationofrna pages 7-9)

HMG-like motif (inference by alignment): A later mechanistic study focused on MEG-3 includes an alignment of an HMG-like motif in MEG-3 and MEG-4, suggesting a conserved ordered motif in both paralogs (in the context of MEG-3’s interaction with PGL proteins). This is supportive but indirect for MEG-4’s mechanism. (schmidt2021proteinbasedcondensationmechanisms pages 2-4)

Critical discrepancy: UniProt “J domain-containing protein”

Across the retrieved primary and review literature focused on MEG-3/MEG-4, MEG-4 is consistently discussed as an intrinsically disordered MEG-family germ plasm protein; none of these sources describe MEG-4 as an Hsp40/J-domain co-chaperone or report J-domain-dependent activities. Accordingly, within the evidence available here, a J-domain annotation is not supported and should be re-verified directly against UniProt/WormBase records (outside this environment). (wang2014regulationofrna pages 5-7, schmidt2021proteinbasedcondensationmechanisms pages 2-4, cipriani2021novellotusdomainproteins pages 1-2)

3) Cellular localization and where MEG-4 acts

Embryonic localization to P granules/germ plasm: MEG-4 is maternally provided and associates with embryonic P granules from the 1-cell through ~100-cell stage, segregating with the P lineage. A study reports experimental tagging of MEG-4 using C-terminal 3×FLAG via CRISPR for localization, supporting that MEG-4 itself is present in embryonic germ plasm granules. (wang2014regulationofrna pages 11-13)

Granule substructure and dynamics (MEG vs PGL): MEG proteins show dynamics distinct from PGL components; MEG-positive/PGL-negative structures can be observed and MEG signals persist longer during disassembly than PGL signals, consistent with multi-phase or structured condensates. (wang2014regulationofrna pages 11-13)

Stage specificity: MEG-3/4 are required for P granule assembly in pre-gastrulation embryos, but perinuclear granules reappear later (L1/L4), indicating MEG-4 is not essential for all later germ-granule assembly modes. (wang2014regulationofrna pages 7-9)

4) Molecular function and biological roles (what MEG-4 does)

Primary functional role: embryonic P granule assembly

Genetic evidence indicates meg-3 and meg-4 are the primary contributors to embryonic (cytoplasmic) P granule assembly. In meg-3 meg-4 zygotes, granule formation is severely impaired, with only transient small posterior granules and loss of robust enrichment in the germline founder cell by later stages. (wang2014regulationofrna pages 9-11, wang2014regulationofrna pages 7-9)

Quantitative phenotype: During the first mitosis, total P granules in meg-3 meg-4 zygotes are reduced to ~11% of wild-type. (wang2014regulationofrna pages 5-7, wang2014regulationofrna media 088f36bf)

Germline mRNA enrichment and inheritance

In wild type, certain maternal RNAs (e.g., nos-2) segregate with P granules. In meg-3 meg-4 embryos, nos-2 RNA segregates symmetrically, consistent with loss of stable P granules, though somatic degradation remains intact. This supports the interpretation that MEG-3/4-dependent P granules contribute to preferential germline enrichment/inheritance of particular maternal mRNAs. (wang2014regulationofrna pages 7-9)

A P-granule transcriptome study further supports that MEG-3/4 are important for concentrating P-granule-associated transcripts in germline blastomeres, and that loss of meg-3/4 can lead to sterility particularly when combined with other germline determinant perturbations (genetic interactions). (lee2020recruitmentofmrnas pages 9-10)

Relationship to translational control and germ cell fate

A 2022 Development paper distinguishes roles of two germ plasm condensates: P granules (MEG-3/4-dependent) and germline P-bodies (MEG-1/2-dependent). In that framework, meg-3 meg-4 mutants lack maternal P granules but do not show the same fate transformation as meg-1 meg-2 mutants; meg-3/4 is described as antagonizing maximal translation activation of certain POS-1 targets in P4, and meg-3 meg-4 mutants remain largely fertile. (cassani2022specializedgermlinepbodies pages 6-8)

5) Pathways and regulators involving MEG-4

Phosphoregulation and genetic epistasis with MBK-2 and PP2A

Genetic epistasis places meg-3/meg-4 downstream of the kinase MBK-2/DYRK and PP2A regulatory subunits PPTR-1/2 for controlling P granule assembly/disassembly. Notably, in mbk-2; meg-3 meg-4 embryos, granules still fail to assemble, indicating MEG-3/4 are required for assembly even when disassembly is inhibited. (wang2014regulationofrna pages 9-11)

The same work provides direct biochemical phosphorylation evidence for MEG-1 and MEG-3 (in vitro kinase assays; phosphoprotein behavior in vivo), and interprets MEG proteins as phosphoregulated scaffolds; however, direct biochemical phosphorylation assays for MEG-4 are not shown in the snippets reviewed here. (wang2014regulationofrna pages 5-7, wang2014regulationofrna pages 15-16)

6) Mutant/RNAi phenotypes and key statistics

Single vs double mutant granule phenotypes

meg-4 single mutants show only a slight reduction in P granule number in zygotes, while meg-3 single mutants show a stronger but still partial phenotype; the meg-3 meg-4 double mutant shows the strongest assembly defects, supporting redundancy with unequal contribution (MEG-3 stronger). (wang2014regulationofrna pages 7-9)

Fertility and germline proliferation

~27–30% sterility is reported for meg-3 meg-4 adults depending on study/assay conditions, implying ~70% remain fertile. (wang2014regulationofrna pages 9-11, cassani2022specializedgermlinepbodies pages 6-8)
A more severe synthetic phenotype is observed when combining MEG defects: meg-1 meg-3 meg-4 animals are reported as 100% sterile, with larvae exhibiting <10 germ cells and failure of germ cell proliferation. (wang2014regulationofrna pages 9-11)

These data argue that MEG proteins contribute redundantly to germline development, and that fertility defects are not explained solely by visible P granule loss (since different meg combinations can be equally sterile with different granule phenotypes). (wang2014regulationofrna pages 15-16)

7) Recent developments (prioritizing 2023–2024)

2024: MEG genes, P granules, and germline-to-soma signaling (UPRmt)

A 2024 Nature Communications study linking germline signals/piRNAs to somatic mitochondrial stress responses states that meg-1, meg-3, and meg-4 are required for cytoplasmic but not perinuclear P granule formation. In that work, RNAi knockdown of meg-1/meg-3/meg-4 did not abolish embryo-lysate-induced activation of UPRmt, whereas perturbing piRNA biogenesis/maturation did suppress the response. This places meg genes (including meg-4) in a broader, contemporary context where P granule integrity intersects with small-RNA biology and organismal stress signaling. (Zhou et al., 2024, https://doi.org/10.1038/s41467-024-53064-0) (zhou2024agermlinetosomasignal pages 1-2)

2023–2024 gap note

Direct 2023–2024 primary papers centered on MEG-4 molecular mechanism were not retrieved in this tool run; the most MEG-4-specific mechanistic genetics remain anchored in earlier landmark studies (2014–2022), while 2024 work uses meg genes largely as perturbations/markers of cytoplasmic P granule assembly. (zhou2024agermlinetosomasignal pages 1-2, wang2014regulationofrna pages 9-11)

8) Current applications and real-world implementations

MEG-4 is primarily used in C. elegans as a genetically tractable handle on embryonic germ plasm/P granule assembly and associated germline mRNA regulation. Common implementation patterns include:

CRISPR allele generation of meg-4 loss-of-function alleles (e.g., frameshift and large deletions) to establish redundancy with meg-3 and to dissect germ granule dynamics. (Wang et al., 2014, https://doi.org/10.7554/eLife.04591; published Dec 2014) (wang2014regulationofrna pages 5-7)
Live imaging of embryonic granules using P granule reporters (e.g., GFP::PGL-1 with nuclear markers) to quantify granule assembly/disassembly and inheritance in meg mutants. (wang2014regulationofrna pages 9-11)
smFISH and protein quantification in P4 to evaluate effects on germline determinants and translational output, leveraging the distinct genetic requirements for P granules (MEG-3/4) versus germline P-bodies (MEG-1/2). (Cassani & Seydoux, 2022, https://doi.org/10.1242/dev.200920; published Nov 2022) (cassani2022specializedgermlinepbodies pages 6-8)
Use of meg RNAi (including meg-4) in newer systems-level studies (e.g., germline-to-soma signaling) to operationally reduce cytoplasmic P granules. (Zhou et al., 2024) (zhou2024agermlinetosomasignal pages 1-2)

9) Expert interpretation and analysis (evidence-weighted)

Most direct evidence supports MEG-4 as a condensate scaffold/regulator rather than an enzyme or transporter. The strong, replicated phenotype is loss of cytoplasmic P granule assembly in embryos when combined with meg-3, plus consequent defects in germline enrichment of maternal mRNAs. (wang2014regulationofrna pages 7-9, lee2020recruitmentofmrnas pages 9-10)
MEG-4’s mechanistic biochemistry is less directly characterized than MEG-3’s. Many in vitro condensation and motif-function experiments are performed on MEG-3; MEG-4 is incorporated chiefly through redundancy genetics and alignment-based inference (e.g., shared HMG-like motif). (schmidt2021proteinbasedcondensationmechanisms pages 2-4)
MEG-dependent fertility likely involves functions beyond visible P granules. Synthetic sterility patterns and comparisons between mutant classes suggest MEG proteins contribute to essential germ plasm activities not strictly equivalent to “having detectable P granules,” consistent with a model where condensates coordinate multiple post-transcriptional regulatory processes. (wang2014regulationofrna pages 15-16, wang2014regulationofrna pages 9-11)

Summary table of key findings

Aspect	Evidence summary	Evidence type	Key citations
Identity/domain	The target is C. elegans meg-4 / C36C9.1 / MEG-4, a close paralog of MEG-3 with 71% identity. Evidence supports MEG-4 as a serine-rich, low-complexity, largely intrinsically disordered protein (~570/832 aa, 69% predicted disordered). Later work aligned a conserved HMG-like motif in MEG-4 with the motif in MEG-3/GCNA proteins. The literature snippets reviewed do not support a J-domain/Hsp40 assignment for MEG-4.	Inference from sequence prediction + comparative/domain analysis; supported by genetics-focused primary literature	(wang2014regulationofrna pages 5-7, schmidt2021proteinbasedcondensationmechanisms pages 2-4, cipriani2021novellotusdomainproteins pages 1-2)
Localization	MEG-4 is maternally provided and associates with embryonic P granules/germ plasm from the 1-cell to ~100-cell stage, segregating with the P lineage. A CRISPR 3×FLAG-tagged MEG-4 was used for localization. MEG-4 is not reported in adult gonad perinuclear granules, and MEG proteins can persist in granules longer than PGL proteins during disassembly; MEG-positive/PGL-negative granules were observed.	Cell biology + genetics	(wang2014regulationofrna pages 11-13)
Molecular/biophysical role	MEG-4 acts redundantly with MEG-3 as a primary factor for assembly of embryonic P granules and enrichment of P-granule-associated mRNAs in germline blastomeres. Loss of meg-3/4 prevents proper localization of PGL droplets and condensation of P-granule mRNAs. The direct biophysical work is stronger for MEG-3, but the evidence supports MEG-4 participating in the same condensate/phase-separation scaffold system.	Genetics + cell biology; partial inference from paralogy and shared phenotypes	(wang2014regulationofrna pages 9-11, wang2014regulationofrna pages 7-9, lee2020recruitmentofmrnas pages 9-10, schmidt2021proteinbasedcondensationmechanisms pages 2-4, schmidt2020coordinationofrna pages 1-4)
Pathways/regulators	Genetic epistasis places meg-4 with meg-3 downstream of MBK-2 and PPTR-1/2 in controlling the balance between P-granule assembly and disassembly. In mbk-2; meg-3 meg-4 embryos, granules still fail to assemble, showing MEG-3/4 are required even when disassembly is blocked. Direct phosphorylation was shown for MEG-1 and MEG-3, but direct biochemical phosphorylation evidence for MEG-4 was not shown in the cited snippets.	Genetics with limited biochemical inference	(wang2014regulationofrna pages 9-11, wang2014regulationofrna pages 11-13, wang2014regulationofrna pages 15-16)
Mutant/RNAi phenotypes	meg-4 single mutants show only a slight reduction in P-granule number, whereas meg-3 meg-4 double mutants have severe embryonic P-granule assembly defects and symmetric segregation of nos-2 RNA. Perinuclear P granules reappear later in PGCs/L1, indicating a stage-specific requirement. meg-3 meg-4 animals show partial sterility, while adding loss of other meg genes can cause severe germline proliferation defects and complete sterility.	Genetics + developmental cell biology	(wang2014regulationofrna pages 9-11, wang2014regulationofrna pages 7-9, cassani2022specializedgermlinepbodies pages 6-8, cipriani2021novellotusdomainproteins pages 1-2)
Key quantitative data	Reported values include: MEG-4 832 aa, 69% predicted disorder (570/832 aa); MEG-3/MEG-4 71% identical; in meg-3 meg-4 zygotes, total P granules during first mitosis are about 11% of wild type; adult sterility is about 27-30% for meg-3 meg-4, with ~70% fertile; meg-1 meg-3 meg-4 mutants are 100% sterile and larvae can have <10 germ cells.	Quantitative genetics/cell biology; sequence-based inference	(wang2014regulationofrna pages 5-7, wang2014regulationofrna pages 7-9, lee2020recruitmentofmrnas pages 9-10, schmidt2021proteinbasedcondensationmechanisms pages 2-4, wang2014regulationofrna pages 9-11)

Table: This table summarizes the evidence-supported functional annotation of C. elegans meg-4/MEG-4, including identity, localization, biological role, regulatory context, and mutant phenotypes. It is restricted to claims directly supported by the cited evidence snippets and highlights where conclusions are based on inference rather than direct MEG-4 biochemistry.

References (URLs and publication dates)

Wang JT et al. “Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans.” eLife (Dec 2014). https://doi.org/10.7554/eLife.04591 (wang2014regulationofrna pages 9-11, wang2014regulationofrna pages 5-7, wang2014regulationofrna pages 7-9, wang2014regulationofrna media 088f36bf)
Lee C-YS et al. “Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins.” eLife (Jan 2020). https://doi.org/10.7554/eLife.52896 (lee2020recruitmentofmrnas pages 9-10)
Schmidt H et al. “Protein-based condensation mechanisms drive the assembly of RNA-rich P granules.” eLife (Jun 2021). https://doi.org/10.7554/eLife.63698 (schmidt2021proteinbasedcondensationmechanisms pages 2-4)
Cassani M, Seydoux G. “Specialized germline P-bodies are required to specify germ cell fate in C. elegans embryos.” Development (Nov 2022). https://doi.org/10.1242/dev.200920 (cassani2022specializedgermlinepbodies pages 6-8)
Zhou L et al. “A germline-to-soma signal triggers an age-related decline of mitochondrial stress response.” Nature Communications (Oct 2024). https://doi.org/10.1038/s41467-024-53064-0 (zhou2024agermlinetosomasignal pages 1-2)

Evidence limitations

No direct UniProt/WormBase record parsing was possible with the available tools; thus, the UniProt “J domain-containing protein” description for Q9TZK8 could not be reconciled against primary literature in this environment. The peer-reviewed literature retrieved here strongly supports a MEG-family intrinsically disordered germ-plasm role and does not mention J-domain/Hsp40 activities for MEG-4. (wang2014regulationofrna pages 5-7, schmidt2021proteinbasedcondensationmechanisms pages 2-4)

References

(wang2014regulationofrna pages 5-7): Jennifer T Wang, Jarrett Smith, Bi-Chang Chen, Helen Schmidt, Dominique Rasoloson, Alexandre Paix, Bramwell G Lambrus, Deepika Calidas, Eric Betzig, and Geraldine Seydoux. Regulation of rna granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in c. elegans. eLife, Dec 2014. URL: https://doi.org/10.7554/elife.04591, doi:10.7554/elife.04591. This article has 438 citations and is from a domain leading peer-reviewed journal.
(wang2014regulationofrna pages 7-9): Jennifer T Wang, Jarrett Smith, Bi-Chang Chen, Helen Schmidt, Dominique Rasoloson, Alexandre Paix, Bramwell G Lambrus, Deepika Calidas, Eric Betzig, and Geraldine Seydoux. Regulation of rna granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in c. elegans. eLife, Dec 2014. URL: https://doi.org/10.7554/elife.04591, doi:10.7554/elife.04591. This article has 438 citations and is from a domain leading peer-reviewed journal.
(wang2014regulationofrna pages 11-13): Jennifer T Wang, Jarrett Smith, Bi-Chang Chen, Helen Schmidt, Dominique Rasoloson, Alexandre Paix, Bramwell G Lambrus, Deepika Calidas, Eric Betzig, and Geraldine Seydoux. Regulation of rna granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in c. elegans. eLife, Dec 2014. URL: https://doi.org/10.7554/elife.04591, doi:10.7554/elife.04591. This article has 438 citations and is from a domain leading peer-reviewed journal.
(wang2014regulationofrna pages 15-16): Jennifer T Wang, Jarrett Smith, Bi-Chang Chen, Helen Schmidt, Dominique Rasoloson, Alexandre Paix, Bramwell G Lambrus, Deepika Calidas, Eric Betzig, and Geraldine Seydoux. Regulation of rna granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in c. elegans. eLife, Dec 2014. URL: https://doi.org/10.7554/elife.04591, doi:10.7554/elife.04591. This article has 438 citations and is from a domain leading peer-reviewed journal.
(wang2014regulationofrna media 088f36bf): Jennifer T Wang, Jarrett Smith, Bi-Chang Chen, Helen Schmidt, Dominique Rasoloson, Alexandre Paix, Bramwell G Lambrus, Deepika Calidas, Eric Betzig, and Geraldine Seydoux. Regulation of rna granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in c. elegans. eLife, Dec 2014. URL: https://doi.org/10.7554/elife.04591, doi:10.7554/elife.04591. This article has 438 citations and is from a domain leading peer-reviewed journal.
(schmidt2021proteinbasedcondensationmechanisms pages 2-4): Helen Schmidt, Andrea Putnam, Dominique Rasoloson, and Geraldine Seydoux. Protein-based condensation mechanisms drive the assembly of rna-rich p granules. eLife, Jun 2021. URL: https://doi.org/10.7554/elife.63698, doi:10.7554/elife.63698. This article has 31 citations and is from a domain leading peer-reviewed journal.
(cipriani2021novellotusdomainproteins pages 1-2): Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, Vinay K Mayya, George Chung, Jia-Xuan Chen, Hala Fahs, Yu Guan, Thomas F Duchaine, Matthias Selbach, Fabio Piano, and Kristin C Gunsalus. Novel lotus-domain proteins are organizational hubs that recruit c. elegans vasa to germ granules. eLife, Jul 2021. URL: https://doi.org/10.7554/elife.60833, doi:10.7554/elife.60833. This article has 32 citations and is from a domain leading peer-reviewed journal.
(wang2014regulationofrna pages 9-11): Jennifer T Wang, Jarrett Smith, Bi-Chang Chen, Helen Schmidt, Dominique Rasoloson, Alexandre Paix, Bramwell G Lambrus, Deepika Calidas, Eric Betzig, and Geraldine Seydoux. Regulation of rna granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in c. elegans. eLife, Dec 2014. URL: https://doi.org/10.7554/elife.04591, doi:10.7554/elife.04591. This article has 438 citations and is from a domain leading peer-reviewed journal.
(lee2020recruitmentofmrnas pages 9-10): Chih-Yung S Lee, Andrea Putnam, Tu Lu, ShuaiXin He, John Paul T Ouyang, and Geraldine Seydoux. Recruitment of mrnas to p granules by condensation with intrinsically-disordered proteins. eLife, Jan 2020. URL: https://doi.org/10.7554/elife.52896, doi:10.7554/elife.52896. This article has 149 citations and is from a domain leading peer-reviewed journal.
(cassani2022specializedgermlinepbodies pages 6-8): Madeline Cassani and Geraldine Seydoux. Specialized germline p-bodies are required to specify germ cell fate in caenorhabditis elegans embryos. Nov 2022. URL: https://doi.org/10.1242/dev.200920, doi:10.1242/dev.200920. This article has 35 citations and is from a domain leading peer-reviewed journal.
(zhou2024agermlinetosomasignal pages 1-2): Liankui Zhou, Liu Jiang, Lan Li, Chengchuan Ma, Peixue Xia, Wanqiu Ding, and Ying Liu. A germline-to-soma signal triggers an age-related decline of mitochondrial stress response. Nature Communications, Oct 2024. URL: https://doi.org/10.1038/s41467-024-53064-0, doi:10.1038/s41467-024-53064-0. This article has 15 citations and is from a highest quality peer-reviewed journal.
(schmidt2020coordinationofrna pages 1-4): Helen Schmidt, Andrea Putnam, Dominique Rasoloson, and Geraldine Seydoux. Coordination of rna and protein condensation by the p granule protein meg-3. bioRxiv, Oct 2020. URL: https://doi.org/10.1101/2020.10.15.340570, doi:10.1101/2020.10.15.340570. This article has 0 citations.

Artifacts

Edison artifact artifact-00

Citations

schmidt2021proteinbasedcondensationmechanisms pages 2-4
wang2014regulationofrna pages 11-13
wang2014regulationofrna pages 7-9
lee2020recruitmentofmrnas pages 9-10
cassani2022specializedgermlinepbodies pages 6-8
wang2014regulationofrna pages 9-11
wang2014regulationofrna pages 15-16
zhou2024agermlinetosomasignal pages 1-2
wang2014regulationofrna pages 5-7
cipriani2021novellotusdomainproteins pages 1-2
schmidt2020coordinationofrna pages 1-4
https://doi.org/10.1038/s41467-024-53064-0
https://doi.org/10.7554/eLife.04591;
https://doi.org/10.1242/dev.200920;
https://doi.org/10.7554/eLife.04591
https://doi.org/10.7554/eLife.52896
https://doi.org/10.7554/eLife.63698
https://doi.org/10.1242/dev.200920
https://doi.org/10.7554/elife.04591,
https://doi.org/10.7554/elife.63698,
https://doi.org/10.7554/elife.60833,
https://doi.org/10.7554/elife.52896,
https://doi.org/10.1242/dev.200920,
https://doi.org/10.1038/s41467-024-53064-0,
https://doi.org/10.1101/2020.10.15.340570,

📄 View Raw YAML

id: Q9TZK8
gene_symbol: meg-4
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: MEG-4 (maternal-effect germline defective 4) is an intrinsically disordered
  protein (IDP) that functions redundantly with its homolog MEG-3 in P granule assembly
  and segregation in C. elegans embryos. MEG-4 contains multiple disordered regions
  enriched in polar and low-complexity sequences, consistent with its role as a scaffold
  for biomolecular condensates. MEG-4 localizes to P granules and is regulated by
  MBK-2/DYRK phosphorylation, which controls P granule dynamics through phase separation.
  While meg-4 single mutants have mild phenotypes, meg-3 meg-4 double mutants fail
  to segregate P granules to the posterior of the zygote, and meg-1 meg-3 meg-4 triple
  mutants are 100% sterile. MEG-4 is essential for RNA recruitment to germ granules
  and proper small RNA homeostasis. Falcon deep research confirms MEG-4 (~71% identical
  to MEG-3, ~69% predicted disorder) is specifically required for cytoplasmic (embryonic)
  P granule assembly but not perinuclear germ granules, which reappear later (L1/L4),
  indicating a stage-specific requirement; in meg-3 meg-4 zygotes total P granules drop
  to ~11% of wild-type and nos-2 mRNA segregates symmetrically. The UniProt name
  "J domain-containing protein" is not supported by the primary literature, which
  describes MEG-4 as an intrinsically disordered MEG-family germ-plasm protein with no
  Hsp40/J-domain co-chaperone activity.
existing_annotations:
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12445390
  review:
    summary: High-throughput yeast two-hybrid screen identified interactions with
      atz-1 and klc-1. The PMID:12445390 publication describes an integrated interactome
      mapping approach for C. elegans germline proteins. While the interaction data
      is valid, the generic term "protein binding" does not provide functional insight
      for a scaffold protein whose core function is phase separation-mediated granule
      assembly.
    action: MARK_AS_OVER_ANNOTATED
    reason: The protein binding annotation from high-throughput Y2H screening is technically
      correct but uninformative. MEG-4 functions as a scaffold protein for P granule
      assembly through phase separation, and its biologically relevant interactions
      (e.g., with MEG-3) involve molecular condensate scaffold activity. Generic "protein
      binding" does not capture this functional context. The specific interactors
      (atz-1, klc-1) from this screen have not been validated for functional relevance
      to P granule biology.
    supported_by:
    - reference_id: PMID:12445390
      supporting_text: we generated a two-hybrid interactome map of the Caenorhabditis
        elegans germline by using 600 transcripts enriched in this tissue
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14704431
  review:
    summary: Large-scale worm interactome mapping study identified MEG-4 interaction
      with ikb-1. This is a high-throughput Y2H screen with independent co-affinity
      purification validation.
    action: MARK_AS_OVER_ANNOTATED
    reason: While the Y2H interaction is experimentally supported, the generic "protein
      binding" term lacks functional specificity. MEG-4 is an IDP scaffold protein
      whose meaningful interactions involve condensate assembly. The interaction with
      ikb-1 (IKK binding protein) has not been shown to be relevant to MEG-4's core
      function in P granule biology. A more informative MF annotation would capture
      the molecular condensate scaffold activity.
    supported_by:
    - reference_id: PMID:14704431
      supporting_text: more than 4000 interactions were identified from high-throughput,
        yeast two-hybrid (HT=Y2H) screens
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19123269
  review:
    summary: Empirically controlled C. elegans interactome study (WI-2007) with quality
      control framework showing interaction data similar in quality to low-throughput
      literature-curated data.
    action: MARK_AS_OVER_ANNOTATED
    reason: This annotation comes from a rigorous high-throughput Y2H study with empirical
      quality control. However, "protein binding" remains an uninformative term for
      MEG-4, whose function depends on its ability to scaffold molecular condensates
      through multivalent interactions mediated by its intrinsically disordered regions.
      The annotation does not capture the functional significance of MEG-4's protein
      interactions.
    supported_by:
    - reference_id: PMID:19123269
      supporting_text: the resulting dataset (Worm Interactome 2007 or WI-2007) is
        similar in quality to low-throughput data curated from the literature
- term:
    id: GO:0051640
    label: organelle localization
  evidence_type: IMP
  original_reference_id: PMID:25535836
  review:
    summary: Wang et al. (2014) demonstrated that MEG proteins regulate P granule
      dynamics through phosphorylation-controlled phase separation. MEG-4 functions
      redundantly with MEG-3 in localizing P granules to the posterior of the embryo
      (PMID:25535836).
    action: ACCEPT
    reason: 'This annotation accurately captures MEG-4''s role in P granule localization.
      The Wang et al. study provides direct mutant phenotype evidence that MEG proteins
      are required for proper organelle localization: "MEG (maternal-effect germline
      defective) proteins are germ plasm components that are required redundantly
      for fertility." P granule segregation to the posterior involves MEG-regulated
      condensation/dissolution dynamics controlled by MBK-2/DYRK kinase and PP2A phosphatase.'
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
        dephosphorylation promotes granule assembly
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        MEG-4 is maternally provided and associates with embryonic P granules from the **1-cell through ~100-cell stage**, segregating with the P lineage.
- term:
    id: GO:1903863
    label: P granule assembly
  evidence_type: IGI
  original_reference_id: PMID:25535836
  review:
    summary: MEG-3 and MEG-4 are required together (genetic interaction) for proper
      P granule assembly. The Wang et al. study shows MEGs stabilize the condensed
      phase of P granules through regulated phase separation.
    action: ACCEPT
    reason: This is a core annotation for MEG-4 function. The IGI evidence code is
      appropriate as meg-3 meg-4 double mutants show synergistic defects in P granule
      assembly not seen in single mutants. MEG proteins localize to a dynamic domain
      surrounding P granules and are direct regulators of granule condensation dynamics
      through their intrinsically disordered, serine-rich regions that undergo phosphorylation-dependent
      phase transitions.
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: GFP-tagged MEG-3 localizes to a dynamic domain that surrounds
        and penetrates each granule
    - reference_id: PMID:25535836
      supporting_text: despite their liquid-like behavior, P granules are non-homogeneous
        structures whose assembly in embryos is regulated by phosphorylation
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        total P granules in meg-3 meg-4 zygotes are reduced to **~11% of wild-type**.
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        MEG-3 and MEG-4 are reported as **~71% identical** and functionally redundant in embryonic P granule assembly.
- term:
    id: GO:0036093
    label: germ cell proliferation
  evidence_type: IGI
  original_reference_id: PMID:25535836
  review:
    summary: MEG proteins are required for germ cell viability and proliferation.
      The meg-1 meg-3 meg-4 triple mutant is 100% sterile, indicating MEGs contribute
      redundantly to germline function.
    action: KEEP_AS_NON_CORE
    reason: While MEG-4 is involved in germ cell proliferation, this represents a
      downstream consequence of its primary function in P granule assembly rather
      than a direct mechanistic role in cell proliferation. The sterility phenotype
      of triple mutants reflects failed germline development due to defective P granule
      function. This is a valid annotation but should be considered non-core compared
      to the direct molecular function in granule assembly.
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: The MEG (maternal-effect germline defective) proteins are germ
        plasm components that are required redundantly for fertility
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        **meg-1 meg-3 meg-4** animals are reported as **100% sterile**, with larvae exhibiting **<10 germ cells** and failure of germ cell proliferation.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25535836
  review:
    summary: Wang et al. identified specific protein interactions for MEG-4 in the
      context of P granule biology, including interactions with MEG-3 and phosphoregulators
      MBK-2 and PP2A(PPTR-1/2).
    action: MODIFY
    reason: While the IPI evidence from PMID:25535836 is more functionally relevant
      than the high-throughput Y2H studies (demonstrating interactions with MEG-3
      and kinase/phosphatase regulators), "protein binding" still fails to capture
      MEG-4's molecular function. MEG-4 functions as a scaffold for molecular condensate
      assembly through its intrinsically disordered regions. The term GO:0140693 "molecular
      condensate scaffold activity" would more accurately describe MEG-4's molecular
      function.
    proposed_replacement_terms:
    - id: GO:0140693
      label: molecular condensate scaffold activity
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: we present evidence that a group of intrinsically disordered,
        serine-rich proteins regulate the dynamics of P granules
    - reference_id: PMID:25535836
      supporting_text: "We demonstrate that MEG-1 and MEG-3 are substrates of the\
        \ kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-\xBD)"
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        MEG-4 is described as a large, serine/threonine-rich protein with extensive predicted disorder and low-complexity regions, consistent with roles as a condensate scaffold/regulator.
- term:
    id: GO:0043186
    label: P granule
  evidence_type: IDA
  original_reference_id: PMID:25535836
  review:
    summary: Direct experimental observation showing MEG-4 localizes to P granules.
      Wang et al. used GFP-tagged MEG proteins and lattice light sheet microscopy
      to demonstrate localization to a dynamic domain surrounding and penetrating
      P granules.
    action: ACCEPT
    reason: This is a well-supported cellular component annotation. IDA evidence from
      imaging studies directly demonstrates MEG-4 localization to P granules. The
      study further characterizes MEG proteins as localizing to a dynamic peripheral
      domain of P granules that regulates condensate assembly/disassembly.
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: GFP-tagged MEG-3 localizes to a dynamic domain that surrounds
        and penetrates each granule
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        A study reports experimental tagging of MEG-4 using **C-terminal 3×FLAG** via CRISPR for localization, supporting that MEG-4 itself is present in embryonic germ plasm granules.
- term:
    id: GO:0140693
    label: molecular condensate scaffold activity
  evidence_type: IDA
  original_reference_id: PMID:25535836
  review:
    summary: MEG-4 is an intrinsically disordered protein that functions as a scaffold
      for P granule condensate assembly. Wang et al. demonstrate that MEG proteins
      regulate granule dynamics through phase separation controlled by phosphorylation.
    action: NEW
    reason: This annotation captures MEG-4's core molecular function as a scaffold
      that promotes the assembly of molecular condensates (P granules) through phase
      separation. MEG-4's long N-terminal intrinsically disordered region with serine-rich,
      polar residue composition (as documented in UniProt features) is characteristic
      of condensate scaffold proteins. The Wang et al. study demonstrates that MEG
      proteins directly regulate P granule condensation/dissolution dynamics through
      phosphorylation-dependent phase transitions.
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: we present evidence that a group of intrinsically disordered,
        serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
    - reference_id: PMID:25535836
      supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
        dephosphorylation promotes granule assembly
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        MEG-4 is predicted to be largely disordered (**~69% predicted disorder; 570/832 aa**)
- term:
    id: GO:0060293
    label: germ plasm
  evidence_type: IDA
  original_reference_id: PMID:25535836
  review:
    summary: MEG-4 is a germ plasm component that localizes to P granules in the posterior
      cytoplasm of early embryos.
    action: NEW
    reason: MEG-4 is explicitly described as a germ plasm component. The germ plasm
      is the specialized cytoplasm inherited by germline precursor cells, and P granules
      are the defining feature of C. elegans germ plasm. This cellular component annotation
      complements the P granule annotation by placing MEG-4 in the broader context
      of germline specification.
    additional_reference_ids:
    - file:worm/meg-4/meg-4-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: The MEG (maternal-effect germline defective) proteins are germ
        plasm components that are required redundantly for fertility
    - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
      supporting_text: |-
        acts **redundantly with its close paralog MEG-3** to drive **cytoplasmic (embryonic) P granule assembly**
references:
- id: PMID:12445390
  title: Integrating interactome, phenome, and transcriptome mapping data for the
    C. elegans germline.
  findings:
  - statement: MEG-4 identified in germline-enriched Y2H interactome screen
    supporting_text: we generated a two-hybrid interactome map of the Caenorhabditis
      elegans germline by using 600 transcripts enriched in this tissue
  - statement: Interactions detected with atz-1 and klc-1
    supporting_text: we find that essential proteins have a tendency to interact with
      each other
- id: PMID:14704431
  title: A map of the interactome network of the metazoan C. elegans.
  findings:
  - statement: Large-scale Y2H interactome mapping
    supporting_text: more than 4000 interactions were identified from high-throughput,
      yeast two-hybrid (HT=Y2H) screens
  - statement: MEG-4 interaction with ikb-1 identified
    supporting_text: Independent coaffinity purification assays experimentally validated
      the overall quality of this Y2H data set
- id: PMID:19123269
  title: Empirically controlled mapping of the Caenorhabditis elegans protein-protein
    interactome network.
  findings:
  - statement: High-confidence interactome data (WI-2007)
    supporting_text: the resulting dataset (Worm Interactome 2007 or WI-2007) is similar
      in quality to low-throughput data curated from the literature
  - statement: Quality control framework validates Y2H data quality
    supporting_text: Through a new quality control empirical framework
- id: PMID:25535836
  title: Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically
    disordered proteins in C. elegans.
  findings:
  - statement: MEG proteins (MEG-1, MEG-3, MEG-4) are IDPs that regulate P granule
      dynamics
    supporting_text: we present evidence that a group of intrinsically disordered,
      serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
  - statement: MEGs are substrates of MBK-2/DYRK kinase and PP2A phosphatase
    supporting_text: "We demonstrate that MEG-1 and MEG-3 are substrates of the kinase\
      \ MBK-2/DYRK and the phosphatase PP2A(PPTR-\xBD)"
  - statement: Phosphorylation promotes granule disassembly, dephosphorylation promotes
      assembly
    supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
      dephosphorylation promotes granule assembly
  - statement: GFP-MEG-3 localizes to dynamic domain surrounding P granules
    supporting_text: GFP-tagged MEG-3 localizes to a dynamic domain that surrounds
      and penetrates each granule
  - statement: MEG proteins function redundantly for fertility
    supporting_text: The MEG (maternal-effect germline defective) proteins are germ
      plasm components that are required redundantly for fertility
- id: file:worm/meg-4/meg-4-deep-research-falcon.md
  title: Falcon deep research report on C. elegans meg-4 (Q9TZK8 / C36C9.1)
  findings:
  - statement: |-
      MEG-4 acts redundantly with its close paralog MEG-3 to drive cytoplasmic
      (embryonic) P granule assembly and to promote preferential germline
      inheritance/enrichment of maternal mRNAs during early embryogenesis.
    supporting_text: |-
      acts **redundantly with its close paralog MEG-3** to drive **cytoplasmic (embryonic) P granule assembly**
    reference_section_type: OTHER
  - statement: |-
      MEG-4 is a large (832 aa), serine/threonine-rich, largely intrinsically
      disordered MEG-family protein (~69% predicted disorder, 570/832 aa) with
      low-complexity regions, consistent with a condensate scaffold/regulator role.
    supporting_text: |-
      MEG-4 is predicted to be largely disordered (**~69% predicted disorder; 570/832 aa**)
    reference_section_type: OTHER
  - statement: |-
      MEG-3 and MEG-4 are approximately 71% identical and functionally redundant
      in embryonic P granule assembly.
    supporting_text: |-
      MEG-3 and MEG-4 are reported as **~71% identical** and functionally redundant in embryonic P granule assembly.
    reference_section_type: OTHER
  - statement: |-
      MEG-4 is maternally provided and associates with embryonic P granules /
      germ plasm from the 1-cell through ~100-cell stage, segregating with the
      P lineage; a CRISPR C-terminal 3xFLAG tag was used to localize MEG-4.
    supporting_text: |-
      MEG-4 is maternally provided and associates with embryonic P granules from the **1-cell through ~100-cell stage**, segregating with the P lineage.
    reference_section_type: OTHER
  - statement: |-
      In meg-3 meg-4 double mutant zygotes, granule formation is severely
      impaired; total P granules during first mitosis are reduced to ~11% of
      wild-type, and nos-2 mRNA segregates symmetrically rather than with the
      germline blastomere.
    supporting_text: |-
      total P granules in meg-3 meg-4 zygotes are reduced to **~11% of wild-type**.
    reference_section_type: OTHER
  - statement: |-
      Genetic epistasis places meg-3/meg-4 downstream of the kinase MBK-2/DYRK
      and PP2A regulatory subunits PPTR-1/2 in controlling the balance of P
      granule assembly and disassembly.
    supporting_text: |-
      Genetic epistasis places *meg-3/meg-4* downstream of the kinase **MBK-2/DYRK** and PP2A regulatory subunits **PPTR-1/2** for controlling P granule assembly/disassembly.
    reference_section_type: OTHER
  - statement: |-
      meg-3/4-dependent P granules contribute to preferential germline
      enrichment/inheritance of particular maternal mRNAs (e.g. nos-2).
    supporting_text: |-
      MEG-3/4-dependent P granules contribute to **preferential germline enrichment/inheritance** of particular maternal mRNAs.
    reference_section_type: OTHER
  - statement: |-
      meg-4 single mutants show only a slight reduction in P granule number;
      the meg-3 meg-4 double mutant has the strongest embryonic assembly defect,
      indicating redundancy with MEG-3 contributing the larger share.
    supporting_text: |-
      *meg-4* single mutants show **only a slight reduction** in P granule number in zygotes
    reference_section_type: OTHER
  - statement: |-
      MEG-1/MEG-3/MEG-4 are required for cytoplasmic but not perinuclear P
      granule formation; perinuclear granules reappear later (L1/L4), indicating
      a stage-specific requirement.
    supporting_text: |-
      **meg-1, meg-3, and meg-4 are required for cytoplasmic but not perinuclear P granule formation**
    reference_section_type: OTHER
  - statement: |-
      meg-1 meg-3 meg-4 triple mutants are 100% sterile with larvae showing
      <10 germ cells and failure of germ cell proliferation, indicating MEG
      proteins contribute redundantly to germline development.
    supporting_text: |-
      **meg-1 meg-3 meg-4** animals are reported as **100% sterile**, with larvae exhibiting **<10 germ cells** and failure of germ cell proliferation.
    reference_section_type: OTHER
  - statement: |-
      The peer-reviewed literature does not support the UniProt "J domain-containing
      protein" name for MEG-4; no source describes MEG-4 as an Hsp40/J-domain
      co-chaperone or reports J-domain-dependent activities.
    supporting_text: |-
      none of these sources describe MEG-4 as an Hsp40/J-domain co-chaperone or report J-domain-dependent activities
    reference_section_type: OTHER
core_functions:
- description: MEG-4 functions as an intrinsically disordered scaffold protein that
    promotes P granule assembly through phase separation. Its long disordered N-terminal
    region with serine-rich, polar residue composition enables multivalent interactions
    required for condensate formation. This is MEG-4's primary molecular function.
  molecular_function:
    id: GO:0140693
    label: molecular condensate scaffold activity
  directly_involved_in:
  - id: GO:1903863
    label: P granule assembly
  locations:
  - id: GO:0043186
    label: P granule
  - id: GO:0060293
    label: germ plasm
  supported_by:
  - reference_id: PMID:25535836
    supporting_text: we present evidence that a group of intrinsically disordered,
      serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
  - reference_id: PMID:25535836
    supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
      dephosphorylation promotes granule assembly
  - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
    supporting_text: |-
      acts **redundantly with its close paralog MEG-3** to drive **cytoplasmic (embryonic) P granule assembly**
  - reference_id: file:worm/meg-4/meg-4-deep-research-falcon.md
    supporting_text: |-
      MEG-4 is described as a large, serine/threonine-rich protein with extensive predicted disorder and low-complexity regions, consistent with roles as a condensate scaffold/regulator.
proposed_new_terms: []
suggested_questions:
- question: Does MEG-4 bind RNA directly, or does it primarily function through protein-protein
    interactions?
- question: What is the precise molecular mechanism by which phosphorylation of MEG-4
    promotes granule disassembly?
- question: Are there MEG-4-specific functions that are distinct from MEG-3, or are
    they fully redundant?
suggested_experiments:
- description: In vitro phase separation assays with purified MEG-4 to characterize
    its intrinsic condensation properties
  hypothesis: MEG-4 can undergo liquid-liquid phase separation in vitro dependent
    on protein concentration and phosphorylation state
  experiment_type: biochemical reconstitution
- description: Phosphomimetic and phospho-null mutations in MEG-4 to map critical
    phosphorylation sites for granule dynamics
  hypothesis: Specific serine residues in MEG-4 are required for MBK-2-dependent regulation
    of P granule assembly
  experiment_type: mutagenesis
- description: CLIP-seq to identify direct RNA targets of MEG-4
  hypothesis: MEG-4 directly binds specific mRNA populations that are recruited to
    P granules
  experiment_type: RNA-protein interaction
- description: Cryo-ET of P granules in wild-type vs meg-4 mutants to characterize
    granule ultrastructure
  hypothesis: MEG-4 contributes to the non-homogeneous internal structure of P granules
  experiment_type: structural biology
tags:
- caeel-p-granules

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Tags

Deep Research

Falcon

Research report: Functional annotation of C. elegans meg-4 (ORF C36C9.1; UniProt Q9TZK8)

Executive summary

1) Key concepts and definitions (current understanding)

Germ plasm, P granules, and condensates

MEG proteins (maternal-effect germline defective)

2) Gene/protein identity verification and domain architecture

Verified identity in the literature

Domain/family features supported by the literature

Critical discrepancy: UniProt “J domain-containing protein”

3) Cellular localization and where MEG-4 acts

4) Molecular function and biological roles (what MEG-4 does)

Primary functional role: embryonic P granule assembly

Germline mRNA enrichment and inheritance

Relationship to translational control and germ cell fate

5) Pathways and regulators involving MEG-4

Phosphoregulation and genetic epistasis with MBK-2 and PP2A

6) Mutant/RNAi phenotypes and key statistics

Single vs double mutant granule phenotypes

Fertility and germline proliferation

7) Recent developments (prioritizing 2023–2024)

2024: MEG genes, P granules, and germline-to-soma signaling (UPRmt)

2023–2024 gap note

8) Current applications and real-world implementations

9) Expert interpretation and analysis (evidence-weighted)

Summary table of key findings

References (URLs and publication dates)

Evidence limitations

Artifacts

Citations

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