Germ-granule components prevent somatic development in the C. elegans germline

Summary

Specialized ribonucleoprotein organelles collectively known as germ granules are found in the germline cytoplasm from worms to humans [1]. In Drosophila, germ granules have been implicated in germline determination [2]. C. elegans germ granules, known as P granules, do not appear to be required for primordial germ cell (PGC) determination [3], but their components are still needed for fertility [4–6]. One potential role for P granules is to maintain germline fate and totipotency. This is suggested by the loss of P granules from germ cells that transform into somatic cell types, e.g. in germlines lacking MEX-3 and GLD-1 or upon neuronal induction by CHE-1 [7, 8]. However, it has not been established whether loss of P granules is the cause or effect of cell-fate transformation. To test cause-effect, we severely compromised P granules by simultaneously knocking down factors that nucleate granule formation (PGL-1 and PGL-3) and promote their perinuclear localization (GLH-1 and GLH-4) [9], and investigated if that causes germ cells to lose totipotency and initiate somatic reprogramming. We found that compromising P granules causes germ cells to express neuronal and muscle markers and send out neurite-like projections, suggesting that P granules maintain totipotency and germline identity by antagonizing somatic fate.

Results and Discussion

The germline cytoplasm of numerous animals contains unique “germ granules”. Despite the discovery of germ granules decades ago, the role(s) of those granules and the fate of germ cells when germ granules are lost are not understood. In Drosophila, loss of germ granules prevents formation of PGCs in embryos [10]. In C. elegans, failure to segregate P granules to the germline blastomeres (P cells) does not impair determination and early development of the germline [3]. Two studies have reported a correlation between transformation of germ cells toward somatic cells and the loss of P granules, suggesting that P granules may function to maintain totipotency in the germline. Upon neuronal induction by the transcription factor CHE-1, P granules are no longer detected in transformed germ cells [8]. Similarly, P granules are lost from germ cells that transform into somatic cell types in mex-3; gld-1 double mutants [7]. MEX-3 and GLD-1 are germline-specific RNA-binding proteins that transiently associate with P granules. In mex-3; gld-1 mutant germlines, P granules persist in germ cells in the distal mitotic zone, but are lost from post-mitotic cells, which transform into somatic cell types [7]. Here we examine whether P-granule impairment is sufficient to cause germ cell reprogramming.

Loss of individual P-granule components in C. elegans results in sterile adults, but the effects of losing P granules altogether have not been fully assessed. This stems in part from the fact that P granules are comprised of dozens of protein components [11, 12], many of which function redundantly; no single mutation has been demonstrated to abolish P granules. We sought to impair P-granule assembly in C. elegans germlines by simultaneously depleting 4 core P-granule components by RNAi. The core P-granule components PGL-1 and PGL-3 self-associate and nucleate granule formation in the cytoplasm [4, 9, 13], while the core components GLH-1 and GLH-4 help promote the localization of granules to the nuclear periphery [9]. Taking advantage of a new approach developed by Gouda et al. [14], we stitched together RNAi constructs for pgl-1, pgl-3, glh-1, and glh-4 and inserted this quadruple construct into a vector for feeding RNAi [15]. RNAi feeding was started on worms in the first larval stage. This initial (P0) generation remained fertile (0/100 sterile), and 29/29 dissected germlines stained positively for PGL-1 (Figure 1A), likely reflecting promotion of germline health by the maternal contribution of P granules and inefficient depletion of PGL-1 in the first generation of RNAi [5, 6, 16]. However, 40/100 of their F1 adult progeny were sterile (sterility ranged from 27% to 89% among experiments; Table S1), with abnormal oocytes and lacking embryos in the uterus (Figure 1B), but still containing sperm as detected by the sperm-specific antibody SP56 (Figure 1C). In fertile F1s, PGL-1 staining was observed in 9/22 dissected germlines; PGL-1 staining was not observed (0/34) in sterile F1 germlines (Figure 1A, p=6.6E-5), suggesting that sterility is correlated with more robust depletion of PGL-1 using this RNAi approach. To determine the extent to which P granules are disrupted, we immunostained sterile F1 germlines for DEPS-1, a constitutive P-granule component that promotes GLH-1 expression and PGL-1 localization to P granules [6]. After P-granule RNAi, DEPS-1 did not localize to granules at the nuclear periphery, but was instead dispersed throughout the cytoplasm (Figure 1D). Transcript levels of pgl-1, pgl-3, glh-1 and glh-4 in germlines dissected from F1 worms after RNAi feeding were reduced 24.7, 13.9, 2.0, and 3.7 fold, respectively (Figure 1E). These results show that core P-granule components are either depleted or dispersed in sterile F1 worms after RNAi feeding.

Figure 1.

P-granule RNAi. A) PGL-1 staining is reduced to below detection in sterile F1 worms following P-granule RNAi. B) Pseudo-colored DIC image showing germ cell abnormalities in sterile F1 hermaphrodites depleted of P granules. C) SP56 staining (red) shows the presence of sperm in P-granule RNAi hermaphrodites. D) DEPS-1, a constitutive P-granule component, is no longer perinuclear following P-granule RNAi but is instead dispersed throughout the cytoplasm. E) Quantitative PCR comparing changes in transcript levels following P-granule RNAi. Error bars show standard deviation. Scale bars are 20 microns.

The pan-neuronal marker unc-119::GFP has been used in other studies to indicate when germ cells have been reprogrammed to a somatic (neural) fate [7, 8]. This marker was used in conjunction with P-granule RNAi to determine if compromising P granules causes germ cells to reprogram toward neurons. Expression of this marker was not observed in the germline of control worms but was observed in the germline of some sterile F1 worms following P-granule RNAi. Based on examination of >200 worms per condition and stage, control worms included empty-vector RNAi P0s and F1 generation worms at the L4 stage and at days 1, 2, and 4 of adulthood; none showed germline GFP expression. Following P-granule RNAi, germline expression of unc-119::GFP was not observed in P0s or L4-stage F1s, but was observed in clusters of cells throughout the germline of sterile F1 adults (Figure 2A): 2.4% of day 1 adults (p=3.5E-2), 10% of day 2 adults (p=3.5E-7), and 17% of day 4 adults (p=4.6E-11). All subsequent P-granule RNAi experiments examined F1 worms on the 2^nd day of adulthood. F1 males at day 2 of adulthood also showed germline unc-119::GFP expression at a similar frequency (5/43 = 12%, Figure 2A). P-granule RNAi hermaphrodites displayed a modest 2-fold increase in unc-119 transcript level in dissected germlines (Figure 1E). To determine if this 2-fold increase in unc-119::GFP transcript level is distributed throughout the germline, or is a result of mosaic unc-119 transcription that correlates with unc-119::GFP-expressing cells, we performed single molecule fluorescent in situ hybridization (smFISH) with an unc-119 probe. FISH signal was not observed in the germline of unc-119::GFP worms (0/20), but was detected in GFP-positive germlines following P-granule RNAi (7/9) (Figure 2B, p=2.3E- 5), suggesting that in wild-type germlines P granules function to destabilize unc-119 transcripts or suppress unc-119 transcription. In germlines that contained unc-119::GFP, unc-119 transcripts were distributed throughout the germline and showed no enrichment in unc-119::GFP-expressing germ cells, suggesting that unc-119::GFP expression is also regulated at the level of translation. Often GFP-expressing germ cells had extended neurite-like projections similar to those reported in mex-3; gld-1 mutant worms [7] (Figure 2C). These results suggest that P granules play a role in maintaining germline totipotency by suppressing expression of somatic factors and somatic differentiation.

Figure 2.

Reprogramming of germ cells toward neurons following P-granule RNAi. A) Expression of the panneuronal unc-119::GFP reporter in the germline (dotted outline) of a hermaphrodite and a male following Pgranule depletion. B) Single molecule FISH of unc-119 mRNA (arrows) and immunostaining of unc-119::GFP expression in the germline. C) High resolution image of germ cells expressing unc-119::GFP and extending neurite-like projections (arrows). D) Expression of the pan-neuronal unc-33::GFP reporter in the germline (dotted outline) following P-granule depletion. Scale bars are 20 microns.

The presence of neurite-like projections following P-granule RNAi suggests that germ cells may be differentiating into specific neuronal subtypes. In C. elegans, the nervous system comprises 37% of the somatic cells in the adult (302 neurons and 56 glial cells) [17]. In addition to pan-neuronal markers like unc- 119::GFP, fluorescent neuronal fate reporters exist for virtually all sensory, motor, and interneuron subtypes. To determine whether transformed germ cells represent a specific type of neuron, P-granule RNAi was performed in lines expressing fluorescent reporters of unc-33 (pan-neuronal), gcy-5, ceh-36, lsy-6 (ASE sensory neurons), cat-1 (dopaminergic and serotonergic neurons), glr-1 (interneurons), cnd-1 (ventral cord motor neurons), unc-47 (GABAergic motor neurons), pttx-3 (AIY interneurons), unc-97 (mechanosensory neurons), and reporters expressed in an unspecified subset of neurons (dhhc-14, nhr-52, unc-93, snb-1 & hlh- 2) (Table S1). Of these lines, the only one to show germline expression after P-granule RNAi was the panneuronal marker unc-33::GFP (Figure 2D, 35/103 sterile worms); none of the terminal neuronal reporters were detectably expressed in the germline following P-granule RNAi. Immunostaining of UNC-10, which is detected in axonal extensions, was not visible in unc-119::GFP-positive germ cells. Additionally, nuclear granules, which are observed in differentiated neurons, were not seen in unc-119::GFP-positive germ cells. Germline expression of the pan-neuronal reporters unc-119 and unc-33 and the appearance of neurite-like projections suggest that some germ cells are reprogrammed to neuron-like cells, but there is no evidence to date that these cells are differentiating into a specific neuronal subtype(s). The absence of reporter gene expression is difficult to interpret, but one possibility is that germ-to-soma reprogramming is being initiated, but not completed, after RNAi depletion of P granules.

To test if P-granule RNAi enhances the ability of germ cells to differentiate into a specific neuronal subtype in response to a neuronal differentiation signal, we used a transgenic strain in which expression of the neuronal differentiation factor CHE-1 can be induced throughout the body by heat shock [8]. CHE-1 is normally expressed in ASE neurons and activates expression of a number of ASE-specific genes [18, 19]. Heat-shock induction of CHE-1 throughout the worm is not sufficient to reprogram cells into ASE neurons in a wild-type background [8]. However, after depletion of any of several chromatin factors (LIN-53, MES-2, MES-3, MES-6, or MES-4) [8, 17], heat-shock induction of CHE-1 can cause germ cells to differentiate into ASE neurons, as marked by ASE-specific gcy-5::GFP expression. Worms carrying hs::CHE-1 with either gcy-5::GFP or unc- 119::GFP reporters were fed control or P-granule RNAi. Germline expression of gcy-5::GFP was observed in 14% of P-granule RNAi worms following heat shock (42/300; p=2.3E-10) (Figure 3A), but in only 1% of control RNAi worms (3/300), showing that depletion of P granules permits CHE-1 expressed in germ cells to drive differentiation of ASE neurons. Germline expression of the pan-neuronal unc-119::GFP reporter was not observed in control RNAi worms (0/100), and expression in P-granule RNAi worms was similar (p=8.2E-1) with (12/100, p=3.4E-4) and without (10/100, p=1.5E-3) heat shock, suggesting that while expression of CHE-1 in the germline of P-granule RNAi worms drives ASE differentiation, it does not increase the frequency of germline reprogramming. These results show that compromising P granules enhances the ability of germ cells to differentiate into neurons in response to CHE-1, and also suggest that only 10–14% of worms contain germ cells that are both sufficiently depleted of P granules using this RNAi method and healthy enough to reprogram into neuron-like cells. An attractive possibility is that LIN-53 and the MES proteins provide a chromatin-level barrier to transcribing neuronal genes in the germline, and that P granules provide a post-transcriptional barrier to translating stochastically-expressed or CHE-1-induced neuronal gene transcripts.

Figure 3.

Reprogramming of mitotic germ cells toward neurons and muscle. A) P-granule RNAi permits gcy-5 expression (arrows) in the germline (dotted outline) after CHE-1 induction. B) Muscle (red) and neuronal (green) markers are detected in germlines following either mex-3; gld-1 RNAi or P-granule RNAi. Both markers are observed in the distal-most region of P-granule RNAi germlines but not of mex-3; gld-1 RNAi germlines. C) The neuronal unc-119::GFP marker is observed in the distal germline of P-granule RNAi worms bearing a glp-1(gf) mutation that extends the distal mitotic zone. D) P-granule RNAi causes germ-towardsoma reprogramming (green) in germlines that contain mitotic cells marked by H3S10ph staining (red). In all panels, arrowheads mark the distal tip of the germline. Scale bars are 20 microns.

We investigated whether P-granule-depleted germlines express markers of multiple somatic lineages, similar to germline teratomas observed following loss of the translational repressors MEX-3 and GLD-1 [7]. As previously reported by Ciosk et al. [7], we observed expression of both unc-119::GFP and a marker of body wall muscle, MYO-3 (detected with the monoclonal 5.6 antibody), in germlines following mex-3; gld-1 RNAi (Figure 3B, MYO-3 in 20/21 unc-119::GFP-positive germlines, p=2.2E-12). We also detected MYO-3 in germlines from sterile worms following P-granule RNAi (4/15), but not following control RNAi (0/39, p=4.3E-3). In P-granule RNAi germlines expressing unc-119::GFP, 18/29 co-expressed MYO-3 (p=2.5E-7), compared to 0/26 following control RNAi. This suggests that germ cells can be reprogrammed toward both neuronal and muscle fates. However, immunostaining of HLH-1, another muscle marker, was not observed in P-granule RNAi germlines. To test for reprogramming toward other somatic lineages, we surveyed a number of fluorescent somatic reporters following P-granule RNAi, including pha-4 and grl-11 (pharynx), myo-2, myo-3, hlh-1, him-4, and unc-97 (muscle), ceh-21 and egl-27 (all somatic cells), vab-3 and hbl-1 (skin, nerve cord, and muscle), and elt-2 and end-3 (intestine). Despite seeing consistent expression of unc-119::GFP in the germline, we did not observe expression of these other reporters, including the myo-3 transcriptional reporter, after P-granule RNAi. Somatic-promoter-driven expression of transgenes may not always be a reliable way to test for expression of somatic factors in the germline, especially in cases of partial reprogramming, as gene expression in germ cells is sensitive to chromatin context, 3’ UTRs, and the presence in transgenes of DNA sequences that are not normally expressed in germ cell [20–22]. At present, our findings suggest that Pgranule depletion using this RNAi technique causes partial but not complete conversion of germ cells toward neurons and muscle. Finding conditions that promote a higher frequency of conversion would facilitate in depth analysis of diverse lineage markers, and targeting different combinations of P-granule components may reveal whether it is the incomplete composition or the disassembly of P granules that causes conversion.

P-granule RNAi causes unc-119::GFP and MYO-3 expression in clusters of cells throughout the germline, including the distal mitotic zone, which is normally occupied by actively dividing germline stem cells (Figure 3B). This pattern is in contrast to mex-3; gld-1 mutant and RNAi germlines, in which reprogramming is observed in the zone normally occupied by meiotic germ cells but not in the distal mitotic zone (Figure 3B) [7]. To determine whether reprogramming occurs in proliferating pre-meiotic germ cells following P-granule RNAi, we introduced the unc-119::GFP reporter into a strain bearing a glp-1 gain-of-function mutation that extends the domain of mitotic germ cells before entry into meiosis [23]. After P-granule RNAi, we observed unc-119::GFP expression in the distal extended-mitotic zone of glp-1(gf) mutant germlines (Figure 3C, glp-1(gf) 7/185, wild-type 8/250). Furthermore, imaging of histone H3 phosphorylated on serine 10 (H3S10ph), a marker of mitosis [24, 25], in P-granule RNAi germlines expressing unc-119::GFP revealed H3S10ph-positive mitotic cells interspersed among unc-119::GFP-positive cells (11/12 dissected germlines). This indicates that reprogramming occurs in germlines undergoing ongoing proliferation but does not rule out the possibility that meiotic germ cells can also be reprogrammed. Our findings distinguish reprogramming after P-granule depletion from reprogramming after loss of MEX-3 and GLD-1: after P-granule depletion, germ cells in the mitotic zone undergo germ-toward-soma reprogramming in both hermaphrodites and males, while reprogramming in mex-3; gld-1 mutants requires entry into meiosis and is not observed in males [7]. Perhaps P granules in the distal germline of mex-3; gld-1 mutants maintain germline stem cell identity and totipotency, and loss of P granules in the meiotic region of those mutants causes reprogramming.

In C. elegans many RNAs are regulated by germline-expressed RNA-binding proteins that transiently associate with P granules [26–30], and in fact maximal repression of some germline-expressed transcripts requires P-granule association of those proteins [31–34], but it has not been clear how the P-granule microenvironment participates in this regulation. In the present study, we simultaneously depleted four key Pgranule components and severely compromised P-granule integrity, in order to infer the function of P granules in germ cells. Our findings support a model in which P granules selectively degrade or impair the translation of mRNAs that promote neuronal and muscle differentiation. Instead of acting as germ cell determinants, P granules likely act to buffer germ cells from the effects of stochastic mis-transcription of genes encoding somatic factors, thereby maintaining germline totipotency and preventing reprogramming of germ cells into somatic cell types. This role may be conserved in mammals, where the germ-granule component Dazl functions in maintenance of pluripotency in mouse primordial germ cells [35]. A critical issue to resolve is how P granules are able to selectively repress somatic, but not germline, factors. One attractive possibility is that selectivity is mediated through small RNAs and P-granule-associated Argonautes, which enable germ cells to distinguish between “self” and “non-self” transcripts (reviewed in [36]). Future experiments will test the contributions of individual P-granule proteins and protein families (e.g. PGL-1 and the PGL family) to preventing germ-toward-soma reprogramming, identify RNAs associated with P granules and the factors that contribute to that association, and elucidate how P granules regulate the turnover and translation of their associated RNAs.

In Brief.

Updike et al. show that compromising germ granules in C. elegans causes germ cells to express neuronal and muscle markers and extend neurite-like projections, suggesting that germ granules maintain totipotency and germline identity by antagonizing somatic fate.

Highlights.

• Depleting germ granules in C. elegans causes germ-toward-soma reprogramming

• Reprogrammed germ cells exhibit characteristics of neurons and muscle

• Model: Germ granules maintain germline totipotency by repressing somatic fate