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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: G5EE07
• Protein Description: RecName: Full=X-box-binding protein 1 {ECO:0000312|WormBase:R74.3};
• Gene Information: Name=xbp-1 {ECO:0000312|WormBase:R74.3}; ORFNames=R74.3 {ECO:0000312|WormBase:R74.3};
• Organism (full): Caenorhabditis elegans.
• Protein Family: Not specified in UniProt
• Key Domains: bZIP. (IPR004827); bZIP_sf. (IPR046347); ER_Stress-Reg_TF. (IPR052470); bZIP_2 (PF07716)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "xbp-1" 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 'xbp-1' 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 xbp-1 (gene ID: xbp-1, UniProt: G5EE07) 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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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: G5EE07
• Protein Description: RecName: Full=X-box-binding protein 1 {ECO:0000312|WormBase:R74.3};
• Gene Information: Name=xbp-1 {ECO:0000312|WormBase:R74.3}; ORFNames=R74.3 {ECO:0000312|WormBase:R74.3};
• Organism (full): Caenorhabditis elegans.
• Protein Family: Not specified in UniProt
• Key Domains: bZIP. (IPR004827); bZIP_sf. (IPR046347); ER_Stress-Reg_TF. (IPR052470); bZIP_2 (PF07716)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "xbp-1" 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 'xbp-1' 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 xbp-1 (gene ID: xbp-1, UniProt: G5EE07) 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.

Research plan and verification
- Identity check: The target is xbp-1 from Caenorhabditis elegans (UniProt G5EE07). Foundational C. elegans studies identify xbp-1 as the IRE-1-dependent UPRER transcription factor; its product is a basic leucine zipper (bZIP) transcription factor that is generated by IRE-1–mediated unconventional splicing and drives ER stress-responsive gene expression (e.g., BiP homologs hsp-3/hsp-4). This agrees with the provided UniProt description and domains (bZIP, ER stress-regulated TF) and confirms the organism and gene symbol mapping (no conflicting genes with the same symbol are cited here) (shen2001complementarysignalingpathways pages 1-2, shen2005geneticinteractionsdue pages 1-2, shen2001complementarysignalingpathways pages 2-3, richardson2011physiologicalire1xbp1and pages 1-2).

Key concepts and definitions (current understanding)
- Molecular function: xbp-1 encodes a transcription factor that is activated by IRE-1 through unconventional mRNA splicing during ER stress. The spliced isoform (XBP-1s) is a potent bZIP transcription factor that induces UPRER genes to increase folding capacity, ER-associated degradation (ERAD), and other proteostasis programs (Shen et al., Cell 2001; Shen et al., PLoS Genet 2005; Richardson et al., PLoS Genet 2011; URLs: https://doi.org/10.1016/S0092-8674(01)00612-2; https://doi.org/10.1371/journal.pgen.0010037; https://doi.org/10.1371/journal.pgen.1002391) (shen2001complementarysignalingpathways pages 1-2, shen2005geneticinteractionsdue pages 1-2, richardson2011physiologicalire1xbp1and pages 1-2).
- Mechanism of activation: The ER-resident sensor IRE-1 detects protein-folding stress, oligomerizes, and activates its endoribonuclease, which splices xbp-1 mRNA to produce XBP-1s. This mechanism is essential for transcriptional induction of UPRER targets in C. elegans (Shen et al., 2001; 2005; URLs above) (shen2001complementarysignalingpathways pages 1-2, shen2005geneticinteractionsdue pages 1-2).
- Downstream outputs/targets: Canonical induced targets include ER HSP70/BiP paralogs hsp-3 and hsp-4; in mixed-stage animals after DTT, hsp-3 is induced approximately 2-fold and hsp-4 approximately 9-fold, with hsp-3 having ~5-fold higher basal expression than hsp-4 (Shen et al., 2001) (shen2001complementarysignalingpathways pages 2-3, shen2001complementarysignalingpathways pages 1-2).
- Cellular and subcellular context: xbp-1 functions within the ER unfolded protein response (UPRER), acting downstream of IRE-1 to drive transcriptional programs that expand ER folding capacity and promote ERAD; PERK/PEK-1 attenuates translation, and ATF-6 contributes to a complementary transcriptional program. All three branches are engaged to maintain ER homeostasis under physiological conditions (Richardson et al., 2011) (richardson2011physiologicalire1xbp1and pages 1-2).

Signaling pathway placement and genetic interactions
- Complementarity and redundancy: In C. elegans, ire-1/xbp-1 and pek-1 (PERK) are functionally complementary (transcriptional induction versus translational attenuation). Loss of either ire-1 or xbp-1 is synthetically lethal with loss of either pek-1 or atf-6, causing L2 developmental arrest, reflecting essential redundancy during development (Shen et al., 2005; URL: https://doi.org/10.1371/journal.pgen.0010037) (shen2005geneticinteractionsdue pages 1-2).
- Quantitative branch contribution: Microarray analysis indicates pek-1 contributes to induction of about 23% of inducible UPR (i-UPR) genes, whereas ire-1/xbp-1 together regulate most i-UPR genes; atf-6 is especially important for constitutive UPR (c-UPR) gene expression during development/homeostasis (Shen et al., 2005) (shen2005geneticinteractionsdue pages 1-2).

Biological roles and phenotypes (development, immunity, neurons, proteostasis, aging)
- Development and baseline ER homeostasis: UPRER is required throughout development. Double impairment (e.g., ire-1 with pek-1) yields early larval arrest and intestinal degeneration, underscoring the developmental requirement for complementary UPRER arms (Shen et al., 2001; 2005) (shen2001complementarysignalingpathways pages 1-2, shen2005geneticinteractionsdue pages 1-2).
- Immunity and physiological stress: XBP-1 deficiency causes constitutive ER stress with elevated basal IRE-1 and PEK-1 activity. The requirements for xbp-1 and pek-1 increase with immune activation and at elevated physiological temperatures; immune activation can be necessary and sufficient to induce lethality in xbp-1-deficient animals, while xbp-1 loss does not necessarily alter pathogen susceptibility directly (Richardson et al., 2011; URL: https://doi.org/10.1371/journal.pgen.1002391) (richardson2011physiologicalire1xbp1and pages 1-2, richardson2011investigatingtherole pages 181-188).
- Neuronal function: Neuron-specific perturbation of IRE-1/XBP-1 causes accumulation of synaptic receptor subunits in the ER (e.g., glutamate receptor trafficking defects), indicating a cell-autonomous role for the UPRER in neuronal proteostasis (Richardson, thesis excerpts) (richardson2011investigatingtherole pages 46-48). A neuron-specific ER-stress model induced by UNC-9 overexpression demonstrated an age-dependent, cell-autonomous IRE-1→XBP-1 UPRER response; p38 MAPK PMK-3 phosphorylates IRE-1 to regulate chronic neuronal ER stress, and insulin signaling acts through autophagy to counter p38–IRE-1–XBP-1 activity (Guan et al., 2020; URL: https://doi.org/10.1371/journal.pgen.1008704) (guan2020alleviatingchronicer pages 1-2).
- Proteostasis and neurodegeneration: Constitutively active XBP-1s ameliorates tauopathy phenotypes in a C. elegans model, whereas loss of xbp-1 exacerbates toxicity; ATF6 and PERK branches also contribute to XBP-1s-mediated protection, likely via ERAD (Waldherr et al., 2019; URL: https://doi.org/10.1038/s41467-019-12070-3) (xu2024theunfoldedprotein pages 4-5).
- Aging: IRE-1 RNase activity (both xbp-1 splicing and RIDD) declines early in adulthood at the onset of reproduction and is not restored by reduced reproduction, indicating an early age-dependent failure of the UPRER sensor that contributes to proteostasis decline (De-Souza et al., 2022; URL: https://doi.org/10.3389/fragi.2022.1044556) (xu2024theunfoldedprotein pages 1-1).

Recent developments and latest research (2023–2024)
- UPRER–DNA damage/replication stress crosstalk (2024): Replication fork stalling (pri-1/pri-2 depletion; HU exposure) activates the UPRER in C. elegans embryos and somatic tissues, with strong hsp-4 induction; functionally, ire-1 and pek-1 are required for somatic resistance to replication stress, whereas embryonic hsp-4 induction can be partially independent of ire-1/xbp-1 and instead require atf-6, revealing branch redundancy under DNA replication stress. Quantitatively, exposure to 15 mM hydroxyurea (HU) from L1 reduced progression past L4 within 48 h in mutants; pri-1/pri-2 RNAi and 10–20 mM HU elicited robust hsp-4::GFP activation (Xu et al., G3, Jan 2024; URL: https://doi.org/10.1093/g3journal/jkae017) (xu2024theunfoldedprotein pages 9-9, xu2024theunfoldedprotein pages 4-5, xu2024theunfoldedprotein pages 10-11, xu2024theunfoldedprotein pages 1-1, xu2024theunfoldedprotein pages 1-2).
- IRE-1 RIDD modifies neuroendocrine signaling (2023 preprint): A C. elegans-specific RIDD activity was demonstrated to degrade the TGFβ-like ligand mRNA daf-7 in sensory neurons in response to extremely low tunicamycin doses, preceding detectable xbp-1 splicing. Brief pre-exposure to low tunicamycin (0.1–0.3 μg/ml; ~100–300× lower than canonical stress doses) increased population size >2-fold at 27°C under environmental stress; the benefit was independent of pek-1 and reversed by daf-7 overexpression, supporting a causal RIDD→daf-7→neuroendocrine mechanism (Ying et al., bioRxiv preprint, Aug 16, 2023; URL: https://doi.org/10.1101/2023.08.10.552841). Note: preprint, not peer-reviewed (ying2023theriddactivity pages 15-17, ying2023theriddactivity pages 1-4).

Current applications and implementations
- Genetic and reporter tools: hsp-4::gfp is widely used to monitor UPRER; Xu 2024 used embryonic and somatic hsp-4 reporters to map branch-specific dependencies under replication stress (Xu et al., 2024) (xu2024theunfoldedprotein pages 4-5, xu2024theunfoldedprotein pages 10-11, xu2024theunfoldedprotein pages 1-1).
- Disease modeling and intervention testing: XBP-1s overexpression serves as a neuroprotective strategy in worm tauopathy models to test ER stress-modulating therapeutics (Waldherr et al., 2019) (xu2024theunfoldedprotein pages 4-5). Neuron-specific models (UNC-9 overexpression) enable dissection of chronic ER stress circuitry (p38→IRE-1 phosphorylation; insulin/autophagy counter-regulation) for translational insight into neurodegenerative disease pathways (Guan et al., 2020) (guan2020alleviatingchronicer pages 1-2).
- Stress preconditioning: Low-dose ER stressors that preferentially engage IRE-1 RIDD may pre-condition worms for environmental stress via neuroendocrine reprogramming (pending peer review) (Ying et al., 2023) (ying2023theriddactivity pages 15-17, ying2023theriddactivity pages 1-4).

Expert analysis and integrated view
- The C. elegans UPRER is organized as complementary signaling modules in which IRE-1→XBP-1 primarily mediates transcriptional remodeling, PEK-1 attenuates translation to reduce ER load, and ATF-6 supports development/homeostasis and can compensate for canonical IRE-1/XBP-1 outputs under specific stresses (e.g., replication stress in embryos). Developmental viability depends on at least two branches; loss of any single branch heightens sensitivity to physiological loads, particularly immune stimulation and heat (Shen et al., 2005; Richardson et al., 2011) (shen2005geneticinteractionsdue pages 1-2, richardson2011physiologicalire1xbp1and pages 1-2, richardson2011investigatingtherole pages 181-188).
- XBP-1’s role in neurons is both cell-autonomous (maintaining secretory proteostasis) and circuit-modulated: chronic neuronal ER stress is gated by p38 MAPK phosphorylation of IRE-1 and countered by insulin-driven autophagy, while IRE-1 RIDD may adjust organismal state via sensory neuroendocrine outputs (Guan et al., 2020; Ying et al., 2023) (guan2020alleviatingchronicer pages 1-2, ying2023theriddactivity pages 15-17, ying2023theriddactivity pages 1-4).
- Aging involves an early decline of IRE-1 RNase activity, diminishing both xbp-1 splicing and RIDD, which likely reduces adaptive proteostasis capacity, with implications for age-associated neurodegeneration where enhancing XBP-1s activity is protective (De-Souza et al., 2022; Waldherr et al., 2019) (xu2024theunfoldedprotein pages 1-1, xu2024theunfoldedprotein pages 4-5).
- Replication stress/DDR crosstalk is an emerging theme: UPRER activation by stalled forks, and the requirement of ire-1 and pek-1 to preserve somatic fitness under HU, underscore a broader role for ER proteostasis in genome stability pathways, with branch redundancy evident in embryos (Xu et al., 2024) (xu2024theunfoldedprotein pages 9-9, xu2024theunfoldedprotein pages 4-5, xu2024theunfoldedprotein pages 10-11, xu2024theunfoldedprotein pages 1-1, xu2024theunfoldedprotein pages 1-2).

Relevant statistics and recent data points
- UPRER target induction: hsp-3 ~2-fold; hsp-4 ~9-fold after DTT; hsp-3 basal ~5× hsp-4 (Shen et al., 2001) (shen2001complementarysignalingpathways pages 2-3, shen2001complementarysignalingpathways pages 1-2).
- Developmental genetics: ire-1(RNAi); pek-1(RNAi) double perturbation led to ~90% L2 arrest by day 6 (n=120) (Shen et al., 2001) (shen2001complementarysignalingpathways pages 2-3).
- Branch-specific contributions: pek-1 required for ~23% of inducible UPR genes by microarray (Shen et al., 2005) (shen2005geneticinteractionsdue pages 1-2).
- Post-transcriptional regulation: NMD inhibition increases xbp-1 mRNA ~2-fold (Richardson et al., 2011) (richardson2011physiologicalire1xbp1and pages 1-2).
- Replication stress assays (2024): Exposure to 15 mM HU from L1 reduced advancement past L4 within 48 h in mutants; pri-1/pri-2 RNAi and 10–20 mM HU produced strong hsp-4::gfp activation; ire-1 and pek-1 required for somatic resistance (Xu et al., 2024) (xu2024theunfoldedprotein pages 9-9, xu2024theunfoldedprotein pages 4-5, xu2024theunfoldedprotein pages 10-11, xu2024theunfoldedprotein pages 1-1).
- RIDD/neuroendocrine preconditioning (2023 preprint): low tunicamycin (0.1–0.3 μg/ml) increased population size >2-fold at 27°C; rescue independent of pek-1 and abrogated by DAF-7 overexpression (Ying et al., 2023) (ying2023theriddactivity pages 15-17, ying2023theriddactivity pages 1-4).

Embedded study summary
| Year | Study (first author) | Context / Model | Main Finding (1–2 sentences) | Quantitative / Notable Data | URL / DOI (Citation) |
|---:|---|---|---|---|---|
| 2001 | Shen | C. elegans; genetic analysis of UPR | IRE-1 mediates unconventional cytoplasmic splicing of xbp-1 mRNA to produce XBP-1 bZIP TF required for UPR activation and normal larval development. | hsp-3 induced ~2-fold and hsp-4 ~9-fold after DTT; ire-1(RNAi)+pek-1(RNAi) → ~90% L2 arrest by day 6 (n=120). | https://doi.org/10.1016/S0092-8674(01)00612-2 (shen2001complementarysignalingpathways pages 2-3) |
| 2005 | Shen | C. elegans; microarray & genetics | ire-1 and xbp-1 jointly regulate most inducible UPR (i-UPR) genes; pek-1 (PERK) controls a distinct subset and is required for ~23% of i-UPR induction; branches show synthetic genetic interactions with atf-6/pek-1. | pek-1 required for ~23% of i-UPR genes (microarray). | https://doi.org/10.1371/journal.pgen.0010037 (shen2005geneticinteractionsdue pages 1-2) |
| 2011 | Richardson | C. elegans; physiology, infection models | XBP-1 deficiency causes constitutive ER stress; IRE-1–XBP-1 and PEK-1 requirements increase with immune activation and temperature, linking UPR to immunity and development. | NMD inhibition (smg-2) increases xbp-1 mRNA ~2-fold; dynamic temperature-dependent genetic sensitivities reported. | https://doi.org/10.1371/journal.pgen.1002391 (richardson2011physiologicalire1xbp1and pages 1-2) |
| 2020 | Guan | C. elegans; neuron-specific ER stress model | Overexpression of neuronal UNC-9 induces chronic, cell-autonomous IRE-1→XBP-1 UPRER; p38 MAPK (PMK-3) phosphorylates IRE-1 to regulate chronic stress, while insulin signaling promotes autophagy to counteract p38–IRE-1–XBP-1. | Age-dependent neuronal response; genetic evidence for PMK-3 → IRE-1 phosphorylation regulating XBP-1 activation. | https://doi.org/10.1371/journal.pgen.1008704 (guan2020alleviatingchronicer pages 1-2) |
| 2019 | Waldherr | C. elegans tauopathy model (transgenic) | Constitutive expression of active XBP-1s (UPRER activation) protects neurons and reduces pathological tau phenotypes; loss of xbp-1 exacerbates tau toxicity. | Constitutive XBP-1s ameliorates tauopathy phenotypes in worm models (see main figures). | https://doi.org/10.1038/s41467-019-12070-3 (xu2024theunfoldedprotein pages 4-5) |
| 2022 | De-Souza | C. elegans; aging assays | IRE-1 endoribonuclease activity (including xbp-1 splicing and RIDD) declines early in adulthood at the onset of reproduction and is not rescued by reduced reproduction, contributing to age-related UPRER decline. | Decline in IRE-1 RNase activity occurs early in adulthood (onset of reproductive period); affects both xbp-1 splicing and RIDD. | https://doi.org/10.3389/fragi.2022.1044556 (xu2024theunfoldedprotein pages 1-1) |
| 2024 | Xu | C. elegans; replication stress / DNA damage (pri-1/pri-2 RNAi, HU) | Replication-fork stalling activates the UPR-ER (hsp-4 induction) and the IRE-1 and PEK-1 branches are required for somatic resistance to replication stress; embryonic hsp-4 induction can be partially IRE-1/XBP-1-independent and involve ATF-6. | Exposure paradigms: 15 mM HU from L1 → reduced progression past L4 within 48 h; 10–20 mM HU and pri-1/pri-2 RNAi induced strong hsp-4::GFP activation. | https://doi.org/10.1093/g3journal/jkae017 (xu2024theunfoldedprotein pages 9-9) |
| 2023 | Ying | C. elegans; RIDD in sensory neurons (bioRxiv) | IRE-1 RIDD degrades the TGF-β–like mRNA daf-7 in sensory neurons at low tunicamycin doses (below those that induce detectable xbp-1 splicing), modulating neuroendocrine signaling to pre-emptively increase stress survival. | Low tunicamycin (0.1–0.3 μg/ml; ~100–300× lower than canonical doses) increased population size >2-fold at 27°C; rescue independent of pek-1 and abrogated by DAF-7 overexpression. | https://doi.org/10.1101/2023.08.10.552841 (ying2023theriddactivity pages 15-17) |

Table: Concise table of foundational and recent C. elegans studies on xbp-1/IRE-1, summarizing models, main conclusions, key quantitative results, and DOI links for quick reference.

References (URLs and dates)
- Shen et al., Complementary signaling pathways regulate the unfolded protein response and are required for C. elegans development. Cell. 2001-12-28; doi:10.1016/S0092-8674(01)00612-2; URL: https://doi.org/10.1016/S0092-8674(01)00612-2 (shen2001complementarysignalingpathways pages 1-2, shen2001complementarysignalingpathways pages 2-3).
- Shen et al., Genetic interactions due to constitutive and inducible gene regulation mediated by the unfolded protein response in C. elegans. PLoS Genet. 2005-09-30; doi:10.1371/journal.pgen.0010037; URL: https://doi.org/10.1371/journal.pgen.0010037 (shen2005geneticinteractionsdue pages 1-2).
- Richardson et al., Physiological IRE-1-XBP-1 and PEK-1 signaling in Caenorhabditis elegans larval development and immunity. PLoS Genet. 2011-11-17; doi:10.1371/journal.pgen.1002391; URL: https://doi.org/10.1371/journal.pgen.1002391 (richardson2011physiologicalire1xbp1and pages 1-2, richardson2011investigatingtherole pages 181-188).
- Guan et al., Alleviating chronic ER stress by p38-Ire1-Xbp1 pathway and insulin-associated autophagy in C. elegans neurons. PLOS Genet. 2020-09-28; doi:10.1371/journal.pgen.1008704; URL: https://doi.org/10.1371/journal.pgen.1008704 (guan2020alleviatingchronicer pages 1-2).
- Waldherr et al., Constitutive XBP-1s-mediated activation of the ER UPR protects against pathological tau. Nat Commun. 2019-09-11; doi:10.1038/s41467-019-12070-3; URL: https://doi.org/10.1038/s41467-019-12070-3 (xu2024theunfoldedprotein pages 4-5).
- De-Souza et al., IRE-1 endoribonuclease activity declines early in C. elegans adulthood and is not rescued by reduced reproduction. Front Aging. 2022-10-26; doi:10.3389/fragi.2022.1044556; URL: https://doi.org/10.3389/fragi.2022.1044556 (xu2024theunfoldedprotein pages 1-1).
- Xu et al., The unfolded protein response of the endoplasmic reticulum protects Caenorhabditis elegans against DNA damage caused by stalled replication forks. G3 (Genes|Genomes|Genetics). Advance access 2024-01-24; doi:10.1093/g3journal/jkae017; URL: https://doi.org/10.1093/g3journal/jkae017 (xu2024theunfoldedprotein pages 9-9, xu2024theunfoldedprotein pages 4-5, xu2024theunfoldedprotein pages 10-11, xu2024theunfoldedprotein pages 1-1, xu2024theunfoldedprotein pages 1-2).
- Ying et al., The RIDD activity of C. elegans IRE1 modifies neuroendocrine signaling in anticipation of environmental stress to ensure survival. bioRxiv preprint. 2023-08-16; doi:10.1101/2023.08.10.552841; URL: https://doi.org/10.1101/2023.08.10.552841 (ying2023theriddactivity pages 15-17, ying2023theriddactivity pages 1-4).

References

1. (shen2001complementarysignalingpathways pages 1-2): Xiaohua Shen, Ronald E. Ellis, Kyungho Lee, Chuan-Yin Liu, Kun Yang, Aaron Solomon, Hiderou Yoshida, Rick Morimoto, David M. Kurnit, Kazutoshi Mori, and Randal J. Kaufman. Complementary signaling pathways regulate the unfolded protein response and are required for c. elegans development. Cell, 107:893-903, Dec 2001. URL: https://doi.org/10.1016/s0092-8674(01)00612-2, doi:10.1016/s0092-8674(01)00612-2. This article has 885 citations and is from a highest quality peer-reviewed journal.

2. (shen2005geneticinteractionsdue pages 1-2): Xiaohua Shen, Ronald E Ellis, Kenjiro Sakaki, and Randal J Kaufman. Genetic interactions due to constitutive and inducible gene regulation mediated by the unfolded protein response in c. elegans. PLoS Genetics, 1:e37, Sep 2005. URL: https://doi.org/10.1371/journal.pgen.0010037, doi:10.1371/journal.pgen.0010037. This article has 311 citations and is from a domain leading peer-reviewed journal.

3. (shen2001complementarysignalingpathways pages 2-3): Xiaohua Shen, Ronald E. Ellis, Kyungho Lee, Chuan-Yin Liu, Kun Yang, Aaron Solomon, Hiderou Yoshida, Rick Morimoto, David M. Kurnit, Kazutoshi Mori, and Randal J. Kaufman. Complementary signaling pathways regulate the unfolded protein response and are required for c. elegans development. Cell, 107:893-903, Dec 2001. URL: https://doi.org/10.1016/s0092-8674(01)00612-2, doi:10.1016/s0092-8674(01)00612-2. This article has 885 citations and is from a highest quality peer-reviewed journal.

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Citations

1. shen2005geneticinteractionsdue pages 1-2
2. richardson2011investigatingtherole pages 46-48
3. guan2020alleviatingchronicer pages 1-2
4. xu2024theunfoldedprotein pages 4-5
5. xu2024theunfoldedprotein pages 1-1
6. shen2001complementarysignalingpathways pages 2-3
7. xu2024theunfoldedprotein pages 9-9
8. ying2023theriddactivity pages 15-17
9. shen2001complementarysignalingpathways pages 1-2
10. richardson2011investigatingtherole pages 181-188
11. xu2024theunfoldedprotein pages 10-11
12. xu2024theunfoldedprotein pages 1-2
13. ying2023theriddactivity pages 1-4
14. https://doi.org/10.1016/S0092-8674(01
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16. https://doi.org/10.1371/journal.pgen.1002391
17. https://doi.org/10.1371/journal.pgen.0010037
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26. https://doi.org/10.1371/journal.pgen.1008704,
27. https://doi.org/10.1093/g3journal/jkae017,
28. https://doi.org/10.1101/2023.08.10.552841,