| Finding | Function/process | Localization | Interactions/partners | Assays/evidence type | Quantitative stats | Primary source (date, URL) |
|---|---|---|---|---|---|---|
| Gene identity and core granule role | DEPS-1 is the product of **deps-1 / Y65B4BL.2**, a constitutive **P-granule-associated protein** required for proper **PGL-1/PGL-3 localization** and thus P-granule assembly | Cytoplasmic in germ cells and **concentrated on P granules** in adult germ line and late embryos; antibody P-granule staining lost in deps-1 mutants | Genetic/functional relationship upstream of **PGL-1/PGL-3**; also influences **GLH-1** accumulation | Positional cloning/rescue, RNAi phenocopy, anti-DEPS-1 immunostaining, DEPS-1::GFP imaging, western blot | DEPS-1 protein ~**69 kDa**; orthologs show **45–51% identity** in related Caenorhabditis spp.; 4 mutant alleles predicted strong LOF/null | **Spike et al., “DEPS-1 promotes P-granule assembly and RNA interference in C. elegans germ cells”** (Mar 2008), Development. https://doi.org/10.1242/dev.015552 |
| Fertility and germ-cell proliferation phenotype | DEPS-1 is required for **fertility**, **gametogenesis**, and normal **germ-cell proliferation** | Germ line / gonad arms | Linked functionally to constitutive P-granule machinery | Mutant phenotype scoring, germ-cell counting, temperature-shift analysis | In **deps-1(bn121) M−Z−** at **24.5°C**, **93% sterile**; **56%** of germline arms had **<200 germ nuclei**; **63%** lacked both sperm and oocytes; mean germ cells/gonad arm **254 ± 236** (n=16, range 10–762) vs wild type **586 ± 45** (n=6, range 526–651) | **Spike et al., 2008** (Mar 2008), Development. https://doi.org/10.1242/dev.015552 |
| Germline RNAi support via RDE-4 | DEPS-1 promotes **germline RNA interference**, likely in part by supporting **rde-4 mRNA/protein accumulation**; RNAi defects are selective for germline/maternal targets | Germline P granules; post-transcriptional role inferred from cytoplasmic granule localization | Functional link to **RDE-4**; overlap with **RDE-3/MUT-2**-repressed gene sets | qRT-PCR, western blot, feeding RNAi assays, microarray comparison | **rde-4 mRNA reduced 7–10-fold** and **RDE-4 protein ~10-fold lower** in deps-1 M−Z− adults; strong resistance to **pos-1/skn-1/pie-1 RNAi**; overlap of upregulated genes with rde-3 dataset: **9/32 (~30%)**, **P < 2.2 × 10⁻⁹**; selected genes upregulated **~4- to 326-fold** | **Spike et al., 2008** (Mar 2008), Development. https://doi.org/10.1242/dev.015552 |
| Direct PRG-1 binding and piRNA-silencing role | DEPS-1 directly couples **P granules** to the **piRNA pathway**; required for **piRNA-dependent silencing** but not primary piRNA biogenesis | Perinuclear granules across adult germline regions; DEPS-1 and PRG-1 form intertwined elongated condensates | Direct interaction with **PRG-1/PIWI** via N-terminal **PBS (PIWI-binding site)** motif | PRG-1 IP-MS, colocalization imaging, MST biophysics, CRISPR PBS deletion, piRNA sensor assay | PRG-1 IP-MS recovered **133 proteins**, DEPS-1 among **top 10** interactors; MST **Kdapp = 855 ± 133 nM** (full-length PRG-1–DEPS-1), **349 ± 45 nM** (PRG-1 PIWI–full-length DEPS-1), **1.9 µM ± 98 nM** (PBS peptide–PRG-1 PIWI); **deps-1 null** and **ΔPBS** mutants desilence piRNA sensor | **Suen et al., “DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans”** (Aug 2020), Nature Communications. https://doi.org/10.1038/s41467-020-18089-1 |
| Condensate ultrastructure and mutator-foci coupling | DEPS-1 organizes **PRG-1 condensate morphology** and helps maintain spatial coupling between **P granules** and **mutator foci** for downstream silencing | Perinuclear P granules; loss of PBS causes DEPS-1 cytoplasmic diffusion and compacted PRG-1 condensates | **PRG-1**, **MUT-16**, additional interactor **EDG-1** | Live imaging, high-resolution microscopy, condensate morphometry, Y2H for EDG-1 | **ΔPBS** protein expressed at ~**70%** of WT; PRG-1 condensates become **more compacted** in deps-1 null/ΔPBS; PRG-1 morphometry sampled **20 condensates from 2 germlines (n=40 per genotype)**; deps-1 mutants show **fewer, brighter MUT-16 foci**; edg-1 knockdown specifically alters DEPS-1 condensates | **Suen et al., 2020** (Aug 2020), Nature Communications. https://doi.org/10.1038/s41467-020-18089-1 |
| Secondary endo-siRNA / 22G homeostasis | DEPS-1 acts **downstream of PRG-1** to promote **secondary 22G endo-siRNAs** from piRNA targets and affects multiple germline small-RNA pathways | Functional bridge between P granules and mutator foci | PRG-1-associated piRNA pathway; effects on **WAGO**, limited on **ERGO-1**, modest/complex on **CSR-1** classes | Small-RNA sequencing, enrichment/overlap analyses, reporter silencing | **21U/piRNA levels remain similar to WT** in deps-1 mutants, whereas prg-1 loses 21Us (**one-sided t-test P < 10⁻²⁰**, n=2); **300/425 WAGO targets** show **>2-fold 22G reduction** (**P < 10⁻¹³⁹**); **7/23 ERGO-1 targets** affected (**P < 0.2**); overlap with reduced CSR-1-target 22Gs **4/162 genes** vs **447/2012** genes with >2-fold reduction (**P < 10⁻¹³**); sequencing often **n=3** biological replicates | **Suen et al., 2020** (Aug 2020), Nature Communications. https://doi.org/10.1038/s41467-020-18089-1 |
| Small RNAs target granule genes and explain transcript effects | DEPS-1 perturbation changes endo-siRNAs targeting granule factors and correlates with mRNA changes | Germline perinuclear granule system | Endo-siRNA targeting of **P-granule factors** broadly | Integrative analysis of small RNA and prior expression data | **8986/11,088** germline-expressed genes are endo-siRNA targets; **55/63** curated P-granule factors are endo-siRNA targets; **10/63** P-granule factors show differential 22Gs in deps-1 mutant; decrease in small RNAs correlates with mRNA increase (**R² = 0.58**, **P < 0.01**) | **Suen et al., 2020** (Aug 2020), Nature Communications. https://doi.org/10.1038/s41467-020-18089-1 |
| Recent nanoscale localization update | 2023 expansion microscopy refines DEPS-1 placement within **protein-dense P granules** and shows **P granule malformation** in deps-1 mutants | DEPS-1 appears as **small clusters localized within P granules**; deps-1 mutants show reduced and sometimes nuclear-membrane-dissociated perinuclear granules | Spatial comparison with **PRG-1**, **MUT-16**, **ZNFX-1** subdomains | Expansion microscopy (EExM), pan-protein staining, anti-DEPS-1/PRG-1 imaging, granule-size normalization | Average granules per nucleus: **2.5 ± 0.8** by GFP-DEPS-1 and **2.8 ± 1.3** by pan-stain (**9 nuclei**, **3 experiments**); average expansion factor **~3×** from **31 expanded nuclei / 6 experiments** vs **47 non-expanded nuclei / 3 experiments**; P granules smaller in **deps-1(bn124)** and **mut-16(pk710)**, with significance **P < 0.001** and **P < 0.0001** depending on comparison | **Suen et al., “Expansion microscopy reveals subdomains in C. elegans germ granules”** (May 2023 preprint), bioRxiv. https://doi.org/10.1101/2022.05.29.493872 |


*Table: This table summarizes core experimental findings for C. elegans DEPS-1, including function, localization, molecular partners, assay types, and quantitative results from the main primary studies. It is designed as a compact evidence map for functional annotation of UniProt Q9N303.*