A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos

Putnam, Andrea; Cassani, Madeline; Smith, Jarrett; Seydoux, Géraldine

doi:10.1038/s41594-019-0193-2

Cited by 211 publications

(282 citation statements)

References 33 publications

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“…We suggest that germ granules are not crucial for RNAi per se, but rather are important for small RNA homeostasis, with consequences that can persist for multiple generations. Previous studies have shown that the stability of the germ granules is affected by environmental changes (for instance temperature 55,56 ), and also that temperature shifts trigger changes in heritable small RNAs 3,57 . Because germ granules impact small RNA biogenesis, the granules could be important mediators in the translation of environmental changes to small RNA-mediated transgenerational memory.…”

Section: Discussionmentioning

confidence: 99%

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

Lev

Toker

et al. 2019

Preprint

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In C. elegans nematodes, components of liquid-like germ granules were shown to be required for transgenerational small RNA inheritance. Surprisingly, we show here that mutants with defective germ granules (pptr-1, meg-3/4, pgl-1) can nevertheless inherit potent small RNA-based silencing responses, but some of the mutants lose this ability after many generations of homozygosity. Animals mutated in pptr-1, which is required for stabilization of P granules in the early embryo, display extremely strong heritable RNAi responses, which last for tens of generations, long after the responses in wild type animals peter out. The phenotype of mutants defective in the core germ granules proteins MEG-3 and MEG-4, depends on the genotype of the ancestors: Mutants that derive from maternal lineages that had functional MEG-3 and MEG-4 proteins exhibit enhanced RNAi inheritance for multiple generations. While functional ancestral meg-3/4 alleles correct, and even potentiates the ability of mutant descendants to inherit RNAi, defects in germ granules functions can be memorized as well; Wild type descendants that derive from lineages of mutants show impaired RNAi inheritance for many (>16) generations, although their germ granules are intact. Importantly, while P granules are maternally deposited, wild type progeny derived from meg-3/4 male mutants also show reduced RNAi inheritance. Unlike germ granules, small RNAs are inherited also from the sperm.Moreover, we find that the transgenerational effects that depend on the ancestral germ granules require the argonaute protein HRDE-1, which carries heritable small RNAs in the germline. Indeed, small RNA sequencing reveals imbalanced levels of many endogenous small RNAs in germ granules mutants. Strikingly, we find that hrde-1;meg-3/4 triple mutants inherit RNAi, although hrde-1 was previously thought to be essential for heritable silencing. We propose that germ granules sort and shape the RNA pool, and that small RNA inheritance memorizes this activity for multiple generations.

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Section: Discussionmentioning

confidence: 99%

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

Lev

Toker

et al. 2019

Preprint

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“…MEG-3 and MEG-4 form gel-like scaffolds that recruit and stimulate the coalescence 67 of P granule proteins in germ plasm to ensure their partitioning to the embryonic germline and the 68 primordial germ cells Z2 and Z3 (Fig. 1;Putnam et al, 2019). In meg-3 meg-4 embryos, P granules do not 69 coalesce in germ plasm, causing granule components to be partitioned equally to all cells and turned 70 over ( Fig.…”

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confidence: 99%

P granules protect RNA interference genes from silencing by piRNAs

Ouyang

Folkmann

Bernard

et al. 2019

Preprint

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15P granules are perinuclear condensates in C. elegans germ cells proposed to serve as hubs for 16 self/non-self RNA discrimination by Argonautes. We report that a mutant (meg-3 meg-4) that does not 17 assemble P granules in primordial germ cells loses competence for RNA-interference over several 18 generations and accumulates silencing small RNAs against hundreds of endogenous genes, including the 19 RNA-interference genes rde-11 and sid-1. In wild-type, rde-11 and sid-1 transcripts are heavily targeted 20 by piRNAs, accumulate in P granules, but maintain expression. In the primordial germ cells of meg-3 21 meg-4 mutants, rde-11 and sid-1 transcripts disperse in the cytoplasm with the small RNA biogenesis 22 machinery, become hyper-targeted by secondary sRNAs, and are eventually silenced. Silencing requires 23 the PIWI-class Argonaute PRG-1 and the nuclear Argonaute HRDE-1 that maintains trans-generational 24 silencing of piRNA targets. These observations support a "safe harbor" model for P granules in 25 protecting germline transcripts from piRNA-initiated silencing. 26 27In the germ cells of animals, dense RNA-protein condensates accumulate on the cytoplasmic 29 face of the nuclear envelope. These condensates, collectively referred to as nuage, contain components 30 of the small RNA (sRNA) machinery that scan germline transcripts for foreign sequences. For example, in 31Drosophila, components of the piRNA machinery in nuage amplify small RNAs that target transcripts 32 from transposable elements for destruction (Huang et al., 2017). In C. elegans, the PIWI-class Argonaute 33 PRG-1 associates with ~15,000 piRNAs encoded in the genome that scan most, if not all, germline 34 1). Segregation of Argonautes and proteins required for 22G-RNA production into distinct nuage 60 compartments (P granules versus Z granules and mutator foci) could also play a role in sorting 22G-RNAs 61 or limiting their production (Wan et al., 2018). A direct test of these hypotheses, however, has been 62 difficult to obtain as complete loss of P granules causes sterility. 63We previously identified a mutant that affects P granule coalescence only during embryogenesis 64 (Wang et al., 2014). MEG-3 and MEG-4 are intrinsically-disordered proteins present in the germ plasm, a 65 specialized cytoplasm that is partitioned with the germ lineage during early embryonic cleavages (Wang 66 3 and Seydoux, 2013). MEG-3 and MEG-4 form gel-like scaffolds that recruit and stimulate the coalescence 67 of P granule proteins in germ plasm to ensure their partitioning to the embryonic germline and the 68 primordial germ cells Z2 and Z3 (Fig. 1;Putnam et al., 2019). In meg-3 meg-4 embryos, P granules do not 69 coalesce in germ plasm, causing granule components to be partitioned equally to all cells and turned 70 over ( Fig. 1; Wang et al., 2014). Despite lacking P granules during embryogenesis, meg-3 meg-4 71 assemble P granules de novo when the primordial germ cells resume divisions in the first larval stage to 72 generate the ~ 2000 germ cells that constitu...

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“…Their liquid-like property is thought to facilitate dynamic internal rearrangements as well as exchange of materials with their surroundings. However, recently a non-dynamic, gel-like scaffold has been found to envelope the liquid-core of P granules (Putnam et al, 2019). Moreover, differences in translational activity between the periphery and the core of the P-bodies have been observed in Drosophila oocytes (Weil et al, 2012).…”

Section: Deps-1 and Prg-1 Ultrastructurementioning

confidence: 99%

Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure inCaenorhabditis elegans

Braukmann

Butler

et al. 2019

Preprint

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Membraneless organelles are platforms for many aspects of RNA biology including small non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise phase separated environments for their function is unclear. To address this question, we investigated how the PIWI-interacting RNA (piRNA) pathway engages with the membraneless organelle P granule in Caenorhabditis elegans. Proteomic analysis of the PIWI protein PRG-1 revealed an interaction with the constitutive P granule 2 protein DEPS-1. Furthermore we identified a novel motif on DEPS-1, PBS, which interacts directly with the Piwi domain of PRG-1. This protein complex forms intertwining ultrastructures to build elongated condensates in vivo. These suborganelle ultrastructures depend on the Piwi-interacting motif of DEPS-1 and mediate piRNA function. Additionally, we identify a novel interactor of DEPS-1, EDG-1, which is required for DEPS-1 condensates to form correctly. We show that DEPS-1 is not required for piRNA biogenesis but piRNA function: deps-1 mutants fail to produce the secondary endo-siRNAs required for the silencing of piRNA targets. Our study reveals how specific protein-protein interactions drive the spatial organisation and function of small RNA pathways within membraneless organelles.as the P-bodies and germ granules (Eulalio et al., 2007;Voronina et al., 2011).

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A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos

Cited by 211 publications

References 33 publications

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

P granules protect RNA interference genes from silencing by piRNAs

Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure inCaenorhabditis elegans

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