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protein_family: Belongs to the RFX family. {ECO:0000255|PROSITE-
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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: Q09555
• Protein Description: RecName: Full=RFX-like transcription factor daf-19; AltName: Full=Abnormal dauer formation protein 19 {ECO:0000312|WormBase:F33H1.1b};
• Gene Information: Name=daf-19 {ECO:0000312|WormBase:F33H1.1b}; ORFNames=F33H1.1 {ECO:0000312|WormBase:F33H1.1b};
• Organism (full): Caenorhabditis elegans.
• Protein Family: Belongs to the RFX family. {ECO:0000255|PROSITE-
• Key Domains: DNA-bd_RFX. (IPR003150); RFX-like. (IPR039779); WH-like_DNA-bd_sf. (IPR036388); WH_DNA-bd_sf. (IPR036390); BCD_RFX (PF25340)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "daf-19" matches the protein description above
2. Verify the organism is correct: Caenorhabditis elegans.
3. Check if protein family/domains align with what you find in literature
4. 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 'daf-19' 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 daf-19 (gene ID: daf-19, UniProt: Q09555) 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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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: Q09555
• Protein Description: RecName: Full=RFX-like transcription factor daf-19; AltName: Full=Abnormal dauer formation protein 19 {ECO:0000312|WormBase:F33H1.1b};
• Gene Information: Name=daf-19 {ECO:0000312|WormBase:F33H1.1b}; ORFNames=F33H1.1 {ECO:0000312|WormBase:F33H1.1b};
• Organism (full): Caenorhabditis elegans.
• Protein Family: Belongs to the RFX family. {ECO:0000255|PROSITE-
• Key Domains: DNA-bd_RFX. (IPR003150); RFX-like. (IPR039779); WH-like_DNA-bd_sf. (IPR036388); WH_DNA-bd_sf. (IPR036390); BCD_RFX (PF25340)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "daf-19" matches the protein description above
2. Verify the organism is correct: Caenorhabditis elegans.
3. Check if protein family/domains align with what you find in literature
4. 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 'daf-19' 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 daf-19 (gene ID: daf-19, UniProt: Q09555) 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.

Plan
We verified identity and domain architecture for daf-19 (UniProt Q09555) and assembled recent primary literature (2023–2024 priority) alongside foundational studies. We synthesized functions, pathways, localization, isoform-specific roles, downstream targets, regulatory logic, applications, expert opinions, and quantitative data.

Comprehensive Research Report: daf-19 (C. elegans; UniProt Q09555)

1) Key concepts and definitions with current understanding
DAF-19 encodes the sole C. elegans member of the RFX (Regulatory Factor X) transcription factor family. It contains the conserved RFX winged-helix DNA-binding domain and regulates transcription through X-box cis-regulatory motifs, activating the ciliome—the gene set for assembly and function of sensory cilia. DAF-19 is required for formation of sensory cilia and broadly controls expression of shared ciliary components (e.g., intraflagellar transport, transition zone), while cell-type-specific ciliary features are co-specified by additional factors and isoforms (e.g., DAF-19M) (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 3-5, brocalruiz2023forkheadtranscriptionfactor pages 1-2).

DAF-19 binds canonical X-boxes (imperfect inverted repeats of two 6-nt half-sites separated by 1–3 nt, consensus GTNRCC N1–3 RGYAAC) and, via its isoform DAF-19M (alone or with DAF-19C), can also recognize X-box motif variants that drive cell-specific programs in IL2 and male-specific ciliated neurons (ahn2022thec.elegans pages 25-26, ahn2022thec.elegans pages 8-10).

2) Recent developments and latest research (2023–2024 prioritized)
- RFX–Forkhead co-regulation of the sensory ciliome: eLife 2023 identified FKH-8 as a Forkhead transcription factor expressed in all ciliated neurons that physically interacts with and synergizes with DAF-19/RFX to co-activate many sensory ciliome genes. The work integrates DAF-19 with a cooperating TF, expanding the regulatory logic beyond RFX-only control and showing that some ciliome reporters are dramatically reduced in daf-19 nulls while others retain residual activity, implying multi-input control (https://doi.org/10.7554/eLife.89702) (brocalruiz2023forkheadtranscriptionfactor pages 3-3, brocalruiz2023forkheadtranscriptionfactor pages 2-3, brocalruiz2023forkheadtranscriptionfactor pages 3-5, brocalruiz2023forkheadtranscriptionfactor pages 18-19, brocalruiz2023forkheadtranscriptionfactor pages 17-18, brocalruiz2023forkheadtranscriptionfactor pages 1-2, brocalruiz2023forkheadtranscriptionfactor pages 9-10).
- Isoform-specific specialization module (DAF-19M): Cell Reports 2022 (latest comprehensive isoform work) defined a DAF-19M-headed regulatory subroutine in IL2 neurons and male-specific neurons that uses an X-box variant to drive ciliary specialization and behavior (nictation, mating). DAF-19M cooperates with DAF-19C for robust expression of IL2 targets (klp-6, cwp-4, osm-9, cil-7). Upstream terminal selectors UNC-86 and CFI-1 regulate daf-19m expression. EMSA/Y1H support preferential binding of DAF-19M±C to variant X-boxes and DAF-19C to canonical X-boxes (https://doi.org/10.1016/j.celrep.2022.110661) (ahn2022thec.elegans pages 8-10, ahn2022thec.elegans pages 25-26, ahn2022thec.elegans pages 1-4, ahn2022thec.elegans pages 10-11).

3) Current applications and real-world implementations
- Ciliopathy gene discovery and motif-based prediction: The DAF-19/X-box framework and the newly recognized FKH-8 cooperation provide a practical strategy to prioritize ciliary genes by motif searches (canonical and variant X-boxes) and combinatorial TF occupancy, aiding discovery of conserved ciliome components relevant to human ciliopathies (brocalruiz2023forkheadtranscriptionfactor pages 3-5, ahn2022thec.elegans pages 25-26).
- Behavioral genetics modules: The DAF-19M module defines an evolutionarily adaptable “regulatory subroutine” that can be ported conceptually to dissect cell-type-specific ciliary functions in other systems. In worms, this has enabled dissection of nictation circuits and male mating neuron specialization (ahn2022thec.elegans pages 1-4, ahn2022thec.elegans pages 10-11).

4) Expert opinions and analysis from authoritative sources
- Swoboda et al. 2000 established daf-19 as the master RFX regulator of sensory ciliogenesis, with daf-19 mutants lacking cilia and showing broad sensory defects. This foundational view frames DAF-19 as activating shared cilia components via X-boxes, while neuron-subtype-specific features are set independently (swoboda2000therfxtypetranscription pages 1-2, swoboda2000therfxtypetranscription pages 3-4).
- eLife 2023 argues that RFX–Forkhead co-regulation of ciliome genes, demonstrated through DAF-19 and FKH-8 in C. elegans sensory neurons, reflects an ancient regulatory logic, generalizable across cilia types and species (https://doi.org/10.7554/eLife.89702) (brocalruiz2023forkheadtranscriptionfactor pages 1-2, brocalruiz2023forkheadtranscriptionfactor pages 3-3, brocalruiz2023forkheadtranscriptionfactor pages 3-5, brocalruiz2023forkheadtranscriptionfactor pages 18-19).
- Cell Reports 2022 positions DAF-19M as the head of an IL2 neuron subroutine, with isoform cooperation and variant X-box recognition as a mechanism for cell-specific ciliary specialization and behavior control (https://doi.org/10.1016/j.celrep.2022.110661) (ahn2022thec.elegans pages 8-10, ahn2022thec.elegans pages 25-26, ahn2022thec.elegans pages 1-4).

5) Relevant statistics and data from recent and foundational studies
- Daf-c penetrance for daf-19 null (m86): 67% dauer at 15°C (n=340), 85% at 20°C (n=216), 98% at 25°C (n=310), vs 0% in WT—all from Molecular Cell 2000 (swoboda2000therfxtypetranscription pages 1-2).
- Cilia morphology loss in daf-19(m86): ASE cilia—0% full-length, 16% very short, 84% absent (WT: 97% full-length), demonstrating essentiality for ciliogenesis (swoboda2000therfxtypetranscription pages 3-4).
- Reporter regulation by DAF-19: Many ciliome reporters—including IFT (che-11/Ift140, osm-1/Ift172, ift-20, che-13/Ift57) and transition-zone (tmem-107, mks-1)—are dramatically reduced in daf-19 nulls; X-box requirement demonstrated using validated enhancers (brocalruiz2023forkheadtranscriptionfactor pages 3-5).
- Isoform cooperation and binding preference: Co-expression of DAF-19M with DAF-19C restores IL2 reporter expression nearly to wild-type, while DAF-19M alone gives partial rescue; EMSA/Y1H show DAF-19C binds canonical X-boxes more strongly, and DAF-19M+C heteromers bind variant X-boxes effectively (ahn2022thec.elegans pages 8-10).
- DAF-19M phenotypes: daf-19m-specific mutants disrupt expression of IL2/male neuron targets (klp-6, osm-9, cwp-4, cil-7) and impair nictation/mating, while general ciliogenesis (dye filling/IFT) can remain intact—indicating specialization rather than core ciliogenesis (wang2010functionalspecializationof pages 5-7, ahn2022thec.elegans pages 8-10).

Functional roles, pathways, localization
- Primary function: DAF-19 is a transcriptional activator for the ciliome. It drives expression of shared ciliary components (IFT machinery, transition-zone proteins) via canonical X-boxes and, through its DAF-19M isoform, directs neuron class–specific specializations via X-box variants (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 3-5, ahn2022thec.elegans pages 8-10, ahn2022thec.elegans pages 25-26).
- Biological processes: Sensory ciliogenesis (formation and maintenance of cilia); specialization of IL2 and male-specific ciliated neurons that underlie nictation and mating behaviors; dauer developmental decision through ciliary sensory inputs (swoboda2000therfxtypetranscription pages 1-2, swoboda2000therfxtypetranscription pages 3-4, wang2010functionalspecializationof pages 5-7, ahn2022thec.elegans pages 10-11).
- Localization and expression: DAF-19C/short isoforms in all ciliated sensory neurons; DAF-19M expressed in IL2 and male-specific ciliated neurons (CEM, RnB, HOB). DAF-19 A/B isoforms are broader in the nervous system and can repress FKH-8 in non-ciliated neurons, preventing ectopic ciliome programs (brocalruiz2023forkheadtranscriptionfactor pages 9-10, wang2010functionalspecializationof pages 5-7, brocalruiz2023forkheadtranscriptionfactor pages 10-11).
- Downstream genes and pathways: Core ciliome/IFT targets include che-11/Ift140, osm-1/Ift172, ift-20, che-13/Ift57; transition-zone components such as tmem-107 and mks-1; dynein-2 associated xbx-1. IL2/male neuron specialization targets include klp-6 (kinesin), osm-9 (TRPV channel), cwp-4, and cil-7; these often carry variant X-boxes whose mutation abolishes expression in IL2/male neurons (brocalruiz2023forkheadtranscriptionfactor pages 3-5, ahn2022thec.elegans pages 8-10).
- Regulatory logic and co-factors: DAF-19 binds X-boxes as homo- or heteromers; DAF-19M and DAF-19C co-operate at variant X-boxes, while DAF-19C favors canonical X-boxes. FKH-8 co-occupies and physically interacts with DAF-19 to co-activate ciliome genes in sensory neurons, and DAF-19 A/B repress FKH-8 in non-ciliated neurons. Upstream, IL2 terminal selectors UNC-86 and CFI-1 activate daf-19m (ahn2022thec.elegans pages 8-10, brocalruiz2023forkheadtranscriptionfactor pages 3-3, brocalruiz2023forkheadtranscriptionfactor pages 10-11, ahn2022thec.elegans pages 10-11).

Validation of gene/protein identity and domains
- Gene symbol and organism: daf-19 in Caenorhabditis elegans matches UniProt Q09555; literature uniformly refers to the C. elegans RFX-like transcription factor for ciliogenesis and sensory neuron gene expression (swoboda2000therfxtypetranscription pages 1-2, swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 1-2).
- Family/domains consistency: All sources identify DAF-19 as an RFX-family TF with an RFX DNA-binding domain (winged-helix) and dimerization features; this aligns with UniProt domain annotations (swoboda2000therfxtypetranscription pages 3-4, ahn2022thec.elegans pages 8-10).
- Ambiguity check: No conflicting gene symbol usage was found that would suggest a different organism/gene; all sources consistently analyze C. elegans daf-19 (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 3-3).

Embedded summary table
| Topic | Key findings | Principal evidence (year/journal) | URLs |
|---|---|---:|---|
| Identity | DAF-19 is the sole RFX-family transcription factor in C. elegans (UniProt Q09555) and a master regulator of ciliome gene expression via X-box motifs. (RFX DNA-binding domain present) | Swoboda et al., 2000 (Molecular Cell); Brocal-Ruiz et al., 2023 (eLife) (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 3-3) | https://www.uniprot.org/uniprot/Q09555 ; https://doi.org/10.1016/S1097-2765(00)80436-0 ; https://doi.org/10.7554/elife.89702 |
| Domains | Contains an RFX DNA-binding domain (winged-helix / DBD) and dimerization features shared across isoforms; binds X-box cis-elements. | Swoboda et al., 2000; Ahn et al., 2022 (Cell Reports) (swoboda2000therfxtypetranscription pages 3-4, ahn2022thec.elegans pages 8-10) | https://doi.org/10.1016/S1097-2765(00)80436-0 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Organism | Caenorhabditis elegans (worm); daf-19 locus corresponds to UniProt Q09555. | UniProt annotation and functional studies (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 1-2) | https://www.uniprot.org/uniprot/Q09555 |
| Isoforms & principal roles | Multiple isoforms (commonly annotated A/B/C/D and M): DAF-19C (general ciliogenesis in ciliated sensory neurons); DAF-19M (IL2 & male-specific neuron specialization for behaviors); A/B isoforms have distinct neuronal roles (repression of ectopic FKH-8). | Wang et al., 2010 (Genetics); Ahn et al., 2022 (Cell Reports); Brocal-Ruiz et al., 2023 (wang2010functionalspecializationof pages 5-7, brocalruiz2023forkheadtranscriptionfactor pages 10-11) | https://doi.org/10.1534/genetics.110.122879 ; https://doi.org/10.1016/j.celrep.2022.110661 ; https://doi.org/10.7554/elife.89702 |
| Partners / cofactors | Physical and functional cooperation with Forkhead TF FKH-8; upstream regulation by terminal selectors UNC-86 and CFI-1 in IL2 neurons. | Brocal-Ruiz et al., 2023 (eLife); Ahn et al., 2022 (Cell Reports) (brocalruiz2023forkheadtranscriptionfactor pages 3-3, ahn2022thec.elegans pages 8-10) | https://doi.org/10.7554/elife.89702 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Binding motif | Canonical X-box: imperfect inverted repeats (GTNRCC N1-3 RGYAAC); DAF-19M recognizes variant X-box motifs (klp-6-type variants) for cell-specific targets. | Swoboda et al., 2000; Ahn et al., 2022 (swoboda2000therfxtypetranscription pages 3-4, ahn2022thec.elegans pages 25-26) | https://doi.org/10.1016/S1097-2765(00)80436-0 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Downstream targets (ciliome / IFT) | Core ciliome/IFT reporters and genes influenced by DAF-19 include che-11 (IFT140), osm-1 (IFT172), ift-20, che-13 (IFT57), xbx-1 (Dync2li), tmem-107, mks-1 (transition-zone), plus IL2/male-specific targets klp-6, osm-9, cwp-4, cil-7. | Reporter analyses and enhancer tests (Swoboda 2000; Brocal-Ruiz 2023; Ahn 2022) (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 3-5, ahn2022thec.elegans pages 8-10) | https://doi.org/10.1016/S1097-2765(00)80436-0 ; https://doi.org/10.7554/elife.89702 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Localization / expression | DAF-19 expression (isoform-dependent): DAF-19C/short isoform enriched in all ciliated sensory neurons; DAF-19M expressed in IL2 neurons and male-specific ciliated neurons (CEM, RnB, HOB); A/B isoforms expressed more broadly and can repress FKH-8 outside ciliated neurons. | Brocal-Ruiz et al., 2023; Wang et al., 2010; Ahn et al., 2022 (brocalruiz2023forkheadtranscriptionfactor pages 1-2, wang2010functionalspecializationof pages 5-7, ahn2022thec.elegans pages 8-10) | https://doi.org/10.7554/elife.89702 ; https://doi.org/10.1534/genetics.110.122879 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Phenotypes | daf-19(m86) null: strong Daf-c (dauer constitutive) and loss/absence of sensory cilia with major sensory defects; daf-19m-specific mutants (e.g., n4132) impair mating/nictation behaviors while general ciliogenesis and dye-filling can remain intact. | Swoboda et al., 2000; Wang et al., 2010; Ahn et al., 2022 (swoboda2000therfxtypetranscription pages 3-4, wang2010functionalspecializationof pages 5-7, ahn2022thec.elegans pages 8-10) | https://doi.org/10.1016/S1097-2765(00)80436-0 ; https://doi.org/10.1534/genetics.110.122879 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Quantitative data / examples | daf-19(m86) dauer formation: 67% at 15°C (n=340), 85% at 20°C (n=216), 98% at 25°C (n=310) (Daf-c); reporter loss: many ciliome enhancer reporters (e.g., ift-20, osm-1, che-11) show dramatically reduced expression in daf-19 nulls. | Swoboda et al., 2000; reporter assays in Brocal-Ruiz et al., 2023 and Ahn et al., 2022 (swoboda2000therfxtypetranscription pages 3-4, brocalruiz2023forkheadtranscriptionfactor pages 3-5, ahn2022thec.elegans pages 8-10) | https://doi.org/10.1016/S1097-2765(00)80436-0 ; https://doi.org/10.7554/elife.89702 ; https://doi.org/10.1016/j.celrep.2022.110661 |
| Coordination with FKH-8 | FKH-8 (Forkhead TF) physically interacts with DAF-19 and synergistically regulates many sensory ciliome genes; loss of both factors has stronger effects than single mutants. | Brocal-Ruiz et al., 2023 (eLife) (brocalruiz2023forkheadtranscriptionfactor pages 3-3) | https://doi.org/10.7554/elife.89702 |
| Regulatory logic / isoform cooperation | DAF-19C provides broad activation at canonical X-boxes (general ciliogenesis); DAF-19M recognizes X-box variants to drive cell-specific ciliary specializations (IL2/male neurons); co-expression or heteromerization (DAF-19M + DAF-19C) can restore target expression efficiently. | Ahn et al., 2022 (Cell Reports); Wang et al., 2010; Ahn et al., 2021/2022 (ahn2022thec.elegans pages 8-10, wang2010functionalspecializationof pages 5-7, ahn2022thec.elegans pages 1-4) | https://doi.org/10.1016/j.celrep.2022.110661 ; https://doi.org/10.1534/genetics.110.122879 |

Table: Compact, citable summary of DAF-19 (UniProt Q09555) covering identity, domains, isoforms, partners, motifs, targets, expression, phenotypes, quantitative examples, and recent findings (2022–2023). Useful as a quick reference linking each key fact to primary evidence. (swoboda2000therfxtypetranscription pages 3-4, ahn2022thec.elegans pages 8-10, brocalruiz2023forkheadtranscriptionfactor pages 3-3)

URLs (selection)
- Swoboda et al., 2000, Molecular Cell: https://doi.org/10.1016/S1097-2765(00)80436-0 (published Mar 2000) (swoboda2000therfxtypetranscription pages 3-4, swoboda2000therfxtypetranscription pages 1-2)
- Ahn et al., 2022, Cell Reports: https://doi.org/10.1016/j.celrep.2022.110661 (published Apr 2022) (ahn2022thec.elegans pages 8-10, ahn2022thec.elegans pages 25-26, ahn2022thec.elegans pages 1-4, ahn2022thec.elegans pages 10-11)
- Brocal-Ruiz et al., 2023, eLife: https://doi.org/10.7554/eLife.89702 (published Jul 2023) (brocalruiz2023forkheadtranscriptionfactor pages 3-3, brocalruiz2023forkheadtranscriptionfactor pages 10-11, brocalruiz2023forkheadtranscriptionfactor pages 2-3, brocalruiz2023forkheadtranscriptionfactor pages 3-5, brocalruiz2023forkheadtranscriptionfactor pages 18-19, brocalruiz2023forkheadtranscriptionfactor pages 17-18, brocalruiz2023forkheadtranscriptionfactor pages 1-2, brocalruiz2023forkheadtranscriptionfactor pages 9-10)

Notes on evidence scope
Where 2023–2024 papers were not available for specific classic findings (e.g., Daf-c penetrance, loss of cilia), the authoritative 2000 Molecular Cell study is cited. Recent 2023 eLife work updates DAF-19’s cooperative logic with FKH-8 and expands target catalogs; 2022 Cell Reports provides the latest comprehensive isoform/rescue/binding evidence for the DAF-19M module. Together these sources provide current mechanistic and quantitative coverage for daf-19 function, localization, isoforms, and pathways.

References

1. (swoboda2000therfxtypetranscription pages 3-4): Peter Swoboda, Haskell T. Adler, and James H. Thomas. The rfx-type transcription factor daf-19 regulates sensory neuron cilium formation in c. elegans. Molecular cell, 5 3:411-21, Mar 2000. URL: https://doi.org/10.1016/s1097-2765(00)80436-0, doi:10.1016/s1097-2765(00)80436-0. This article has 430 citations and is from a highest quality peer-reviewed journal.

2. (brocalruiz2023forkheadtranscriptionfactor pages 3-5): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

3. (brocalruiz2023forkheadtranscriptionfactor pages 1-2): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

4. (ahn2022thec.elegans pages 25-26): Soungyub Ahn, Heeseung Yang, Sangwon Son, Hyun Sik Lee, Dongjun Park, Hyunsoo Yim, Hee-Jung Choi, Peter Swoboda, and Junho Lee. The c. elegans regulatory factor x (rfx) daf-19m module: a shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Reports, 39:110661, Apr 2022. URL: https://doi.org/10.1016/j.celrep.2022.110661, doi:10.1016/j.celrep.2022.110661. This article has 10 citations and is from a highest quality peer-reviewed journal.

5. (ahn2022thec.elegans pages 8-10): Soungyub Ahn, Heeseung Yang, Sangwon Son, Hyun Sik Lee, Dongjun Park, Hyunsoo Yim, Hee-Jung Choi, Peter Swoboda, and Junho Lee. The c. elegans regulatory factor x (rfx) daf-19m module: a shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Reports, 39:110661, Apr 2022. URL: https://doi.org/10.1016/j.celrep.2022.110661, doi:10.1016/j.celrep.2022.110661. This article has 10 citations and is from a highest quality peer-reviewed journal.

6. (brocalruiz2023forkheadtranscriptionfactor pages 3-3): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

7. (brocalruiz2023forkheadtranscriptionfactor pages 2-3): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

8. (brocalruiz2023forkheadtranscriptionfactor pages 18-19): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

9. (brocalruiz2023forkheadtranscriptionfactor pages 17-18): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

10. (brocalruiz2023forkheadtranscriptionfactor pages 9-10): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

11. (ahn2022thec.elegans pages 1-4): Soungyub Ahn, Heeseung Yang, Sangwon Son, Hyun Sik Lee, Dongjun Park, Hyunsoo Yim, Hee-Jung Choi, Peter Swoboda, and Junho Lee. The c. elegans regulatory factor x (rfx) daf-19m module: a shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Reports, 39:110661, Apr 2022. URL: https://doi.org/10.1016/j.celrep.2022.110661, doi:10.1016/j.celrep.2022.110661. This article has 10 citations and is from a highest quality peer-reviewed journal.

12. (ahn2022thec.elegans pages 10-11): Soungyub Ahn, Heeseung Yang, Sangwon Son, Hyun Sik Lee, Dongjun Park, Hyunsoo Yim, Hee-Jung Choi, Peter Swoboda, and Junho Lee. The c. elegans regulatory factor x (rfx) daf-19m module: a shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Reports, 39:110661, Apr 2022. URL: https://doi.org/10.1016/j.celrep.2022.110661, doi:10.1016/j.celrep.2022.110661. This article has 10 citations and is from a highest quality peer-reviewed journal.

13. (swoboda2000therfxtypetranscription pages 1-2): Peter Swoboda, Haskell T. Adler, and James H. Thomas. The rfx-type transcription factor daf-19 regulates sensory neuron cilium formation in c. elegans. Molecular cell, 5 3:411-21, Mar 2000. URL: https://doi.org/10.1016/s1097-2765(00)80436-0, doi:10.1016/s1097-2765(00)80436-0. This article has 430 citations and is from a highest quality peer-reviewed journal.

14. (wang2010functionalspecializationof pages 5-7): Juan Wang, Hillel T Schwartz, and Maureen M Barr. Functional specialization of sensory cilia by an rfx transcription factor isoform. Genetics, 186:1295-1307, Dec 2010. URL: https://doi.org/10.1534/genetics.110.122879, doi:10.1534/genetics.110.122879. This article has 50 citations and is from a domain leading peer-reviewed journal.

15. (brocalruiz2023forkheadtranscriptionfactor pages 10-11): Rebeca Brocal-Ruiz, Ainara Esteve-Serrano, Carlos Mora-Martínez, Maria Luisa Franco-Rivadeneira, Peter Swoboda, Juan J Tena, Marçal Vilar, and Nuria Flames. Forkhead transcription factor fkh-8 cooperates with rfx in the direct regulation of sensory cilia in caenorhabditis elegans. eLife, Jul 2023. URL: https://doi.org/10.7554/elife.89702, doi:10.7554/elife.89702. This article has 13 citations and is from a domain leading peer-reviewed journal.

Citations

1. swoboda2000therfxtypetranscription pages 1-2
2. swoboda2000therfxtypetranscription pages 3-4
3. brocalruiz2023forkheadtranscriptionfactor pages 3-5
4. brocalruiz2023forkheadtranscriptionfactor pages 3-3
5. brocalruiz2023forkheadtranscriptionfactor pages 1-2
6. brocalruiz2023forkheadtranscriptionfactor pages 2-3
7. brocalruiz2023forkheadtranscriptionfactor pages 18-19
8. brocalruiz2023forkheadtranscriptionfactor pages 17-18
9. brocalruiz2023forkheadtranscriptionfactor pages 9-10
10. wang2010functionalspecializationof pages 5-7
11. brocalruiz2023forkheadtranscriptionfactor pages 10-11
12. https://doi.org/10.7554/eLife.89702
13. https://doi.org/10.1016/j.celrep.2022.110661
14. https://www.uniprot.org/uniprot/Q09555
15. https://doi.org/10.1016/S1097-2765(00
16. https://doi.org/10.7554/elife.89702
17. https://doi.org/10.1534/genetics.110.122879
18. https://doi.org/10.1016/s1097-2765(00
19. https://doi.org/10.7554/elife.89702,
20. https://doi.org/10.1016/j.celrep.2022.110661,
21. https://doi.org/10.1534/genetics.110.122879,