mut-16

id: O62011
gene_symbol: mut-16
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: MUT-16 is a glutamine/asparagine (Q/N)-rich scaffold protein essential
  for the formation of Mutator foci, perinuclear phase-separated condensates that
  serve as sites for siRNA amplification in the C. elegans germline. MUT-16 nucleates
  the assembly of the mutator complex, recruiting RNA-dependent RNA polymerase RRF-1
  and other mutator proteins to form a specialized RNA processing compartment. Through
  its scaffold function, MUT-16 is required for RNA interference (RNAi) and the silencing
  of more than 2,000 endogenous genes, including transposable elements. Mutator foci
  are adjacent to, but distinct from, P granules, and both represent key germline
  RNA regulatory compartments.
existing_annotations:
- term:
    id: GO:1990633
    label: mutator focus
  evidence_type: IDA
  original_reference_id: PMID:22713602
  review:
    summary: MUT-16 localizes to punctate foci at the periphery of germline nuclei,
      termed Mutator foci (PMID:22713602). This is the defining paper that characterized
      Mutator foci as a distinct subcellular compartment. MUT-16 is not merely a component
      but is specifically required for the formation of Mutator foci - in its absence,
      these foci fail to form.
    action: ACCEPT
    reason: This is a core annotation supported by direct experimental evidence. PMID:22713602
      demonstrates that MUT-16 localizes to Mutator foci using fluorescent protein
      tagging and microscopy. The paper establishes that MUT-16 is essential for Mutator
      foci formation, making this localization annotation highly accurate.
    supported_by:
    - reference_id: PMID:22713602
      supporting_text: Here we show that each of the six mutator proteins localizes
        to punctate foci at the periphery of germline nuclei. The Mutator foci are
        adjacent to P granules but are not dependent on core P-granule components
        or other RNAi pathway factors for their formation or stability.
    - reference_id: PMID:22713602
      supporting_text: The glutamine/asparagine (Q/N)-rich protein MUT-16 is specifically
        required for the formation of a protein complex containing the mutator proteins,
        and in its absence, Mutator foci fail to form at the nuclear periphery.
- term:
    id: GO:1990633
    label: mutator focus
  evidence_type: IDA
  original_reference_id: PMID:24684932
  review:
    summary: PMID:24684932 confirms MUT-16 localization to Mutator foci and its role
      in nucleating the mutator complex. The study demonstrates that MUT-16 is the
      scaffold for the mutator complex that silences more than 2,000 C. elegans genes.
    action: ACCEPT
    reason: This annotation is well-supported. PMID:24684932 provides additional evidence
      for MUT-16 localization to Mutator foci while investigating the roles of MUT-14
      and SMUT-1 DEAD box helicases that function in this compartment.
    supported_by:
    - reference_id: PMID:24684932
      supporting_text: More than 2,000 C. elegans genes are targeted for RNA silencing
        by the mutator complex, a specialized small interfering RNA (siRNA) amplification
        module which is nucleated by the Q/N-rich protein MUT-16.
    - reference_id: PMID:24684932
      supporting_text: The mutator complex localizes to Mutator foci adjacent to P
        granules at the nuclear periphery in germ cells.
- term:
    id: GO:1990633
    label: mutator focus
  evidence_type: IDA
  original_reference_id: PMID:32338603
  review:
    summary: PMID:32338603 further characterizes Mutator foci as phase-separated condensates
      and confirms MUT-16 localization. This study identifies SIMR-1 foci as distinct
      from but adjacent to both P granules and Mutator foci.
    action: ACCEPT
    reason: Provides additional confirmation of MUT-16 localization to Mutator foci
      and adds the important characterization that these are phase-separated condensates,
      consistent with MUT-16's Q/N-rich intrinsically disordered regions.
    supported_by:
    - reference_id: PMID:32338603
      supporting_text: SIMR-1 also localizes to distinct subcellular foci adjacent
        to P granules and Mutator foci, two phase-separated condensates that are the
        sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA
        amplification, respectively.
- term:
    id: GO:0003674
    label: molecular_function
  evidence_type: ND
  original_reference_id: GO_REF:0000015
  review:
    summary: This is a placeholder annotation indicating no specific molecular function
      has been assigned. However, based on current literature, MUT-16 functions as
      a molecular condensate scaffold that nucleates assembly of the mutator complex.
    action: MODIFY
    reason: MUT-16 has a well-characterized molecular function as a scaffold protein
      that brings together components of the mutator complex through its Q/N-rich
      intrinsically disordered regions, promoting phase separation and complex assembly.
      This function is analogous to molecular condensate scaffold activity.
    proposed_replacement_terms:
    - id: GO:0140693
      label: molecular condensate scaffold activity
    supported_by:
    - reference_id: PMID:22713602
      supporting_text: The glutamine/asparagine (Q/N)-rich protein MUT-16 is specifically
        required for the formation of a protein complex containing the mutator proteins,
        and in its absence, Mutator foci fail to form at the nuclear periphery.
    - reference_id: PMID:24684932
      supporting_text: More than 2,000 C. elegans genes are targeted for RNA silencing
        by the mutator complex, a specialized small interfering RNA (siRNA) amplification
        module which is nucleated by the Q/N-rich protein MUT-16.
- term:
    id: GO:0030422
    label: siRNA processing
  evidence_type: IMP
  original_reference_id: PMID:22713602
  review:
    summary: MUT-16 is required for siRNA amplification. Genes with high siRNA levels
      (indicative of multiple amplification rounds) are disproportionally affected
      in mut-16 mutants. RdRP RRF-1 colocalizes with MUT-16 at Mutator foci.
    action: ACCEPT
    reason: The GO term siRNA processing includes siRNA amplification by RNA-dependent
      RNA polymerase according to the term definition. PMID:22713602 provides strong
      evidence that MUT-16 is required for this process, with mutants showing disproportionate
      effects on genes requiring siRNA amplification.
    supported_by:
    - reference_id: PMID:22713602
      supporting_text: The RdRP RRF-1 colocalizes with MUT-16 at Mutator foci, suggesting
        a role for Mutator foci in siRNA amplification.
    - reference_id: PMID:22713602
      supporting_text: Furthermore, we demonstrate that genes that yield high levels
        of siRNAs, indicative of multiple rounds of siRNA amplification, are disproportionally
        affected in mut-16 mutants compared with genes that yield low levels of siRNAs.
    - reference_id: PMID:22713602
      supporting_text: We propose that the mutator proteins and RRF-1 constitute an
        RNA processing compartment required for siRNA amplification and RNA silencing.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:12906791
  review:
    summary: PMID:12906791 was an early genome-wide screen that identified mut-16
      as required for transposon silencing. The nuclear localization annotation may
      be imprecise - Mutator foci are actually in the perinuclear cytoplasm, adjacent
      to the nuclear envelope, not within the nucleus.
    action: MODIFY
    reason: Later studies (PMID:22713602) clearly established that MUT-16 localizes
      to perinuclear Mutator foci in the germline cytoplasm, adjacent to P granules.
      These foci are at the nuclear periphery but in the cytoplasm, not inside the
      nucleus. The more precise annotation is to mutator focus (GO:1990633).
    proposed_replacement_terms:
    - id: GO:1990633
      label: mutator focus
    supported_by:
    - reference_id: PMID:22713602
      supporting_text: Here we show that each of the six mutator proteins localizes
        to punctate foci at the periphery of germline nuclei.
    - reference_id: PMID:22713602
      supporting_text: The Mutator foci are adjacent to P granules but are not dependent
        on core P-granule components or other RNAi pathway factors for their formation
        or stability.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:12906791
  review:
    summary: MUT-16 is indeed cytoplasmic, specifically in perinuclear Mutator foci.
      While technically correct, this annotation is too general given the specific
      localization to Mutator foci that is now well-established.
    action: KEEP_AS_NON_CORE
    reason: The cytoplasm annotation is technically correct since Mutator foci are
      cytoplasmic structures at the nuclear periphery. However, it is less informative
      than the mutator focus annotation (GO:1990633) which captures the specific subcellular
      localization.
    supported_by:
    - reference_id: PMID:22713602
      supporting_text: Here we show that each of the six mutator proteins localizes
        to punctate foci at the periphery of germline nuclei.
- term:
    id: GO:0035194
    label: regulatory ncRNA-mediated post-transcriptional gene silencing
  evidence_type: IMP
  original_reference_id: PMID:12906791
  review:
    summary: PMID:12906791 identified mut-16 in a genome-wide screen for genes involved
      in transposon silencing, demonstrating a role in gene silencing. MUT-16 is required
      for the mutator pathway that produces secondary siRNAs for post-transcriptional
      gene silencing.
    action: ACCEPT
    reason: This is a core function of MUT-16. The mutator complex synthesizes secondary
      siRNAs (22G-RNAs) that mediate post-transcriptional gene silencing of transposons
      and other endogenous targets. PMID:12906791 demonstrates mut-16 mutants have
      defective transposon silencing, and later work confirms this is through the
      siRNA pathway.
    supported_by:
    - reference_id: PMID:12906791
      supporting_text: We identified 27 such genes, among which are mut-16, a mutator
        that was previously found but not identified at the molecular level
    - reference_id: PMID:12906791
      supporting_text: Interestingly, the transposon-silencing mechanism shares factors
        with the RNAi machinery.
    - reference_id: PMID:22713602
      supporting_text: We propose that the mutator proteins and RRF-1 constitute an
        RNA processing compartment required for siRNA amplification and RNA silencing.
- term:
    id: GO:0010526
    label: transposable element silencing
  evidence_type: IMP
  original_reference_id: PMID:12906791
  review:
    summary: MUT-16 is required for transposon silencing in the C. elegans germline.
      PMID:12906791 identified mut-16 in a genome-wide screen for genes required to
      silence Tc1 transposon activity.
    action: NEW
    reason: This annotation is not currently in the GOA file but represents a core
      function of MUT-16. The original screen that named mut-16 as a MUTator gene
      was based on transposon activation phenotypes. This is a more specific annotation
      than the general gene silencing term.
    supported_by:
    - reference_id: PMID:12906791
      supporting_text: To better understand the mechanism of transposon silencing,
        we performed a genome-wide RNAi screen for genes that, when silenced, cause
        transposition of Tc1 in the C. elegans germline. We identified 27 such genes,
        among which are mut-16, a mutator that was previously found but not identified
        at the molecular level
references:
- id: GO_REF:0000015
  title: Use of the ND evidence code for Gene Ontology (GO) terms
  findings: []
- id: PMID:12906791
  title: A genome-wide screen identifies 27 genes involved in transposon silencing
    in C. elegans.
  findings:
  - statement: mut-16 was identified in a genome-wide RNAi screen for transposon silencing
      factors
    supporting_text: We identified 27 such genes, among which are mut-16, a mutator
      that was previously found but not identified at the molecular level
  - statement: mut-16 mutants show activation of Tc1 transposon in the germline
    supporting_text: To better understand the mechanism of transposon silencing, we
      performed a genome-wide RNAi screen for genes that, when silenced, cause transposition
      of Tc1 in the C. elegans germline.
  - statement: The transposon-silencing mechanism shares factors with the RNAi machinery
    supporting_text: Interestingly, the transposon-silencing mechanism shares factors
      with the RNAi machinery.
- id: PMID:22713602
  title: MUT-16 promotes formation of perinuclear mutator foci required for RNA silencing
    in the C. elegans germline.
  findings:
  - statement: MUT-16 is a Q/N-rich protein required for Mutator foci formation
    supporting_text: The glutamine/asparagine (Q/N)-rich protein MUT-16 is specifically
      required for the formation of a protein complex containing the mutator proteins,
      and in its absence, Mutator foci fail to form at the nuclear periphery.
  - statement: Mutator foci are punctate foci at the periphery of germline nuclei
    supporting_text: Here we show that each of the six mutator proteins localizes
      to punctate foci at the periphery of germline nuclei.
  - statement: Mutator foci are adjacent to but distinct from P granules
    supporting_text: The Mutator foci are adjacent to P granules but are not dependent
      on core P-granule components or other RNAi pathway factors for their formation
      or stability.
  - statement: RdRP RRF-1 colocalizes with MUT-16 at Mutator foci
    supporting_text: The RdRP RRF-1 colocalizes with MUT-16 at Mutator foci, suggesting
      a role for Mutator foci in siRNA amplification.
  - statement: Genes with high siRNA levels are disproportionally affected in mut-16
      mutants
    supporting_text: Furthermore, we demonstrate that genes that yield high levels
      of siRNAs, indicative of multiple rounds of siRNA amplification, are disproportionally
      affected in mut-16 mutants compared with genes that yield low levels of siRNAs.
  - statement: Mutator foci are required for siRNA amplification
    supporting_text: We propose that the mutator proteins and RRF-1 constitute an
      RNA processing compartment required for siRNA amplification and RNA silencing.
- id: PMID:24684932
  title: MUT-14 and SMUT-1 DEAD box RNA helicases have overlapping roles in germline
    RNAi and endogenous siRNA formation.
  findings:
  - statement: More than 2,000 genes are targeted by the mutator complex
    supporting_text: More than 2,000 C. elegans genes are targeted for RNA silencing
      by the mutator complex, a specialized small interfering RNA (siRNA) amplification
      module which is nucleated by the Q/N-rich protein MUT-16.
  - statement: MUT-16 nucleates the mutator complex
    supporting_text: More than 2,000 C. elegans genes are targeted for RNA silencing
      by the mutator complex, a specialized small interfering RNA (siRNA) amplification
      module which is nucleated by the Q/N-rich protein MUT-16.
  - statement: The mutator complex localizes to Mutator foci at the nuclear periphery
    supporting_text: The mutator complex localizes to Mutator foci adjacent to P granules
      at the nuclear periphery in germ cells.
- id: PMID:32338603
  title: A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted
    mRNAs in C. elegans.
  findings:
  - statement: Mutator foci are phase-separated condensates
    supporting_text: SIMR-1 also localizes to distinct subcellular foci adjacent to
      P granules and Mutator foci, two phase-separated condensates that are the sites
      of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification,
      respectively.
  - statement: Mutator foci are sites of mutator complex-dependent siRNA amplification
    supporting_text: SIMR-1 also localizes to distinct subcellular foci adjacent to
      P granules and Mutator foci, two phase-separated condensates that are the sites
      of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification,
      respectively.
  - statement: SIMR-1 foci are distinct from but adjacent to Mutator foci
    supporting_text: SIMR-1 also localizes to distinct subcellular foci adjacent to
      P granules and Mutator foci, two phase-separated condensates
core_functions:
- molecular_function:
    id: GO:0140693
    label: molecular condensate scaffold activity
  description: MUT-16 is a Q/N-rich intrinsically disordered protein that nucleates
    the assembly of the mutator complex. In the absence of MUT-16, Mutator foci fail
    to form (PMID:22713602). The mutator complex forms through phase separation as
    a perinuclear condensate (PMID:32338603).
  locations:
  - id: GO:1990633
    label: mutator focus
  directly_involved_in:
  - id: GO:0030422
    label: siRNA processing
  - id: GO:0035194
    label: regulatory ncRNA-mediated post-transcriptional gene silencing
  supported_by:
  - reference_id: PMID:22713602
    supporting_text: The glutamine/asparagine (Q/N)-rich protein MUT-16 is specifically
      required for the formation of a protein complex containing the mutator proteins,
      and in its absence, Mutator foci fail to form at the nuclear periphery.
  - reference_id: PMID:24684932
    supporting_text: More than 2,000 C. elegans genes are targeted for RNA silencing
      by the mutator complex, a specialized small interfering RNA (siRNA) amplification
      module which is nucleated by the Q/N-rich protein MUT-16.
tags:
- caeel-p-granules