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C. elegans germ granules regulate both germline and somatic RNAome [miRNA-Seq]

ABSTRACT: Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE228857 | GEO | 2023/07/20

REPOSITORIES: GEO

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C. elegans germ granules regulate both germline and somatic RNAome [RNA-Seq]

Project description:Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.

2023-07-20 | GSE228858 | GEO

Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans

Project description:Using C. elegans germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two previously uncharacterized LOTUS-domain proteins. Loss of eggd-1 and eggd-2 results in separation of P granules from nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.

2021-11-11 | PXD027998 | Pride

The TDRD5/7-like protein, LOTR-1, functions within Z granules to balance epigenetic signals in the Caenorhabditis elegans germline

Project description:LOTUS and Tudor domain containing proteins have critical roles in the germline. Proteins that contain these domains, such as Tejas/Tapas in Drosophila, help localize Vasa to the germ granules and facilitate piRNA transposon mediated silencing. The homologous proteins in mammals, TDRD5 and TDRD7, are required during spermiogenesis. Until now, LOTUS + Tudor domain proteins in C. elegans have remained elusive. Here we describe LOTR-1 (D1081.7), which derives its name from its LOTUS and Tudor domains. Interestingly, LOTR-1 docks next to P granules to colocalize with the Z-granule component ZNFX-1. LOTR-1’s Z-granule association requires its Tudor domain, but both LOTUS and Tudor deletions affect brood size when coupled with a knockdown of the Vasa homolog glh-1. LOTR-1 IP-mass spectrometry confirmed a Tudor-dependent association with Z-granule proteins ZNFX-1 and WAGO-1, but also with germ-granule proteins DEPS-1, the piRNA Argonaute PRG-1, and other WAGO-class Argonautes. Like znfx-1, lotr-1 mutants redistribute the coverage of 22G-RNAs toward the 5’ end of mutator targets and impact transgenerational epigenetic inheritance. Unlike znfx-1, the 5’ shift in 22G-RNA coverage does not extend to CSR-1 targets. Combined, these results suggest that LOTR-1 facilitates interactions between PRG-1/WAGO-class Argonautes, ZNFX-1 and target 3’UTRs to balance 22G-RNA distribution across mutator targets.

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Spatiotemporal regulation of liquid-like condensates in epigenetic inheritance

Project description:Non-membrane bound organelles such as nucleoli, processing bodies, cajal bodies, and germ granules form via spontaneous self-assembly of specific proteins and RNAs. How these biomolecular condensates form and interact are poorly understood. Here we identify two proteins (ZNFX-1 and WAGO-4) that localize to C. elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1/WAGO-4 separate from P granules to define an independent liquid-like condensate that we term the Z granule. In adult germ cells, Z granules assemble into ordered tri-droplet assemblages with P granules and Mutator foci that we term the PZM granule. Finally, we show that one biological function of ZNFX-1 and WAGO-4 is to interact with RNAs in the C. elegans germline to promote transgenerational epigenetic inheritance (TEI). We speculate that the temporal and spatial ordering of liquid droplet organelles may help cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI.

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2020-06-01 | GSE116367 | GEO

elli-1 gene expression array

Project description:Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity. In C. elegans they are called P granules; without them, the germline undergoes partial masculinization or aberrant differentiation. One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes. Loss of CSR-1 or components of its pathway results in a very specific, enlarged P-granule phenotype. In a forward screen to identify mutants with abnormal P granules, ten alleles were recovered with csr-1 P-granule phenotypes, eight of which contain mutations in known CSR-1 pathway components (csr-1, ego-1, ekl-1, and drh-3). The remaining two alleles are in a novel gene now called elli-1 (enlarged germline granules). ELLI-1 is first expressed in primordial germ cells during mid-embryogenesis and continues to be expressed in the adult germline. While ELLI-1 forms cytoplasmic aggregates, they occasionally dock, but do not co-localize with P granules. Instead, the majority of ELLI-1 aggregates accumulate in the shared germline cytoplasm. In elli-1 mutants, several genes that promote RNAi and P-granule accumulation are upregulated, and embryonic lethality, sterility, and RNAi resistance in a hypomorphic drh-3 allele is enhanced. Like mutations in other CSR-1 pathway components, elli-1 is an enhancer of glp-1 sterility, suggesting that ELLI-1 functions with the CSR-1 pathway to modulate RNAi activity, P-granule accumulation, and post-transcriptional expression in the germline.

2016-06-08 | GSE82322 | GEO

Transcriptome profiling of P-granule-depleted or P-granule mutant gonads versus control gonads over time

Project description:The germ cells of multicellular organisms protect their developmental potential through specialized mechanisms. A shared feature of germ cells from worms to humans is the presence of non-membrane-bound ribonucleoprotein organelles called germ granules. Depletion of germ granules in Caenorhabditis elegans (i.e., P granules) leads to sterility and in some germlines expression of the neuronal transgene unc-119::gfp and the muscle myosin MYO-3. Thus, P granules are hypothesized to maintain germ cell totipotency by preventing somatic development, although the mechanism by which P granules carry out this function is unknown. In this study, we performed transcriptome and single molecule RNA-FISH analyses of dissected P-granule-depleted gonads at different developmental stages. Our results demonstrate that P granules are necessary for adult germ cells to down-regulate spermatogenesis RNAs and to prevent the accumulation of numerous soma-specific RNAs. P-granule-depleted gonads that express the unc-119::gfp transgene also express many other genes involved in neuronal development and concomitantly lose expression of germ cell fate markers. Finally, we show that removal of either of two critical P-granule components, PGL-1 or GLH-1, is sufficient to cause germ cells to express UNC-119::GFP and MYO-3 and to display RNA accumulation defects similar to those observed after depletion of P granules. Our data identify P granules as critical modulators of the germline transcriptome and guardians of germ cell fate.

2016-12-22 | GSE92690 | GEO

Germ granule association drives small RNA specificity for a nuclear Argonaute protein

Project description:RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, the majority of RNAi pathway proteins localize to perinuclear, phase-separated germ granules, which are comprised of sub-domains referred to as P granules, Mutator foci, Z granules, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we demonstrate that HRDE-2 localizes to SIMR foci and interacts with the germline nuclear RNAi Argonaute HRDE-1. Furthermore, HRDE-1 also localizes to SIMR foci, dependent on HRDE-2, but only in its small RNA unbound state. This germ granule localization is critical to promote the small RNA binding specificity of HRDE-1 and, in the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, resulting in H3K9me3 deposition on CSR-target genes. Thus, our study demonstrates that HRDE-2 is critical to ensure that the correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.

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P bodies coat germ granules to promote transgenerational gene silencing in C. elegans

Project description:Formation of biomolecular condensates have emerged as a critical mechanism for compartmentation in living cells. Despite interactions between distinct condensates have been reported, the biological relevance of such interactions remains elusive. In germ cells, small RNA silencing factors are enriched in germ granules, which distinct factors are organized into sub-compartments with specific functions linked to genome surveillance or transgenerational gene silencing. Here we showed that perinuclear germ granules are coated by P body, another condensate known for housing untranslated mRNAs and mRNA degradation factors. Disruption of P body factors, including CGH-1/DDX6 and CAR-1/LSM14, lead to dispersal of small RNA factors from perinuclear germ granules and disorganization of sub-compartments within germ granules. We further showed that CAR-1 promote the interactions between CGH-1 with germ granule factors and such interactions are critical for CGH-1’s ability to promote piRNA-mediated gene silencing. Importantly, we observed that cgh-1 mutants are competent in triggering gene silencing but exhibit defects in maintaining gene silencing effects in the subsequent generations. Small RNA sequencing further showed that cgh-1 mutants exhibit defects in amplifying secondary small RNAs, a known carrier of gene silencing memory. Together, our results uncover the function of P body factors in small RNA-mediated transgenerational gene silencing and highlight how the formation and function of one condensate can be regulated by an adjacent, interacting condensate in cells.

2023-06-16 | PXD037342 | Pride

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