The CCR4 deadenylase acts with Nanos and Pumilio in the fine-tuning of Mei-P26 expression to promote germline stem cell self-renewal

Abstract

Translational regulation plays an essential role in Drosophila ovarian germline stem cell (GSC) biology. GSC self-renewal requires two translational repressors, Nanos (Nos) and Pumilio (Pum), which repress the expression of differentiation factors in the stem cells. The molecular mechanisms underlying this translational repression remain unknown. Here, we show that the CCR4 deadenylase is required for GSC self-renewal and that Nos and Pum act through its recruitment onto specific mRNAs. We identify mei-P26 mRNA as a direct and major target of Nos/Pum/CCR4 translational repression in the GSCs. mei-P26 encodes a protein of the Trim-NHL tumor suppressor family that has conserved functions in stem cell lineages. We show that fine-tuning Mei-P26 expression by CCR4 plays a key role in GSC self-renewal. These results identify the molecular mechanism of Nos/Pum function in GSC self-renewal and reveal the role of CCR4-NOT-mediated deadenylation in regulating the balance between GSC self-renewal and differentiation.

Figure 1

CCR4 Is Expressed in the GSCs and Is Required for Their Self-Renewal (A) Schematic representation of a germarium. GSC, germline stem cell; CB, cystoblast; TF, terminal filament, CC, cap cell; and FSC, follicle stem cell. (B) Schematic representation of the twin locus, twin^DG24102, twin⁴¹, and twin⁸¹¹⁵ mutants. Black boxes indicate exons. The arrow indicates the transcription start site. The P-Hobo (yHw) transposable element (not drawn to scale) inserted in twin^DG24102 is shown. The coordinates of the insertion sites are 20027036 for twin^DG24102 and 20032277 for twin⁸¹¹⁵, according to the AE014297 sequence in NCBI. (C–D′) Expression of CCR4 in GSCs. Wild-type (C and C′) and twin^DG24102 mutant (D and D′) germaria labeled with anti-CCR4 antibody (red) and 1B1 (green), which marks the spectrosome and fusome. The merge is shown in C′ and D′. Right panels show higher magnifications of the anterior tips of germaria shown in the left panels. White arrows indicate GSCs. (E–G) twin mutant phenotype of loss of GSCs. Wild-type (E) and twin^DG24102 (F and G) mutant germaria labeled with 1B1 (green) and anti-Vasa antibody (red). Vasa is used as a germ cell marker. White arrows indicate GSCs. (F) Lack of GSCs and the presence of a differentiating cyst. (G) Lack of GSCs and germ cells. Scale bars represent 20 μm in (C–G). (H) Quantification of germaria containing at least one GSC in different twin mutant and control genotypes in 3-, 7-, 14-, and 21-day-old females. n represents the number of germaria scored. See also Figure S1.

Figure 2

twin Is Cell-Autonomously Required in GSC Self-Renewal (A) Clonal twin mutant GSCs do not self-renew. Control (top panel) and twin^DG24102 (bottom panel) mosaic germaria labeled with GFP (green) and 1B1 (red) 7 days after clone induction. Clonal cells, marked by the lack of GFP, are outlined with white dotted lines. (B) Quantification of germaria containing at least one clonal GSC 3, 7, 14, and 21 days after clone induction (n = 111 to 497 germaria). (C–E) Rescue of twin mutant phenotype of GSC loss with CCR4 expression in germ cells. Wild-type (C); twin^DG24102, nos-Gal4/twin^DG24102 (D); twin^DG24102, nos-Gal4/twin^DG24102, UASp-CCR4-HA (E) labeled with 1B1 (green) and anti-Vasa (red). White arrows indicate GSCs. Scale bars represent 20 μm in (A) and (C–E). (F) Quantification of germaria containing at least one GSC in twin mutant and rescued contexts, in 3-, 7-, 14-, and 21-day-old females. n represents the number of germaria scored. See also Figure S2.

Figure 3

twin Genetically and Physically Interacts with nos and pum in GSCs (A) Quantification of germaria containing at least one GSC in twin mutant 3- and 7-day-old females, in combination or not with pum or nos heterozygous mutants. n represents the number of germaria scored. (B) Coimmunoprecipitations with CCR4-HA in GSC-like cells. Ovarian extracts from bam^Δ86 and bam^Δ86, nos-Gal4/bam^Δ86, UASp-CCR4-HA flies were immunoprecipitated with anti-HA, either in the absence or the presence (right panel, RNase) of RNase A. Western blots were revealed with anti-CCR4, anti-Pum, and anti-Nos antibodies. (C) Coimmunoprecipitations with Pum in GSC-like cells. Ovarian extracts from bam^Δ86 flies were immunoprecipitated with anti-Pum (Pum IP) or mock immunoprecipitated (Mock IP), either in the absence or the presence (RNase) of RNase A. Western blots were revealed with anti-Pum, anti-CCR4, and anti-Nos antibodies. The asterisk marks a nonspecific band recognized by the anti-Pum antibody in the input. Input is the protein extract (1/25) prior to immunoprecipitation in (B) and (C). See also Figure S3.

Figure 4

twin Function Is Epistatic to bam (A and B) Bam levels are not upregulated in twin mutant GSCs. Wild-type (A) and twin^DG24102 (B) germaria labeled with anti-Bam antibody (green). The merges between anti-Bam (green), DAPI (blue), and 1B1 (red) are shown in (A′) and (B′). White arrows indicate GSCs. (C and D) twin bam double mutant GSCs can differentiate. bam^Δ86 (C and C′) and Df(3R)Exel6198, bam^Δ86/twin⁴¹, bam^Δ86 (D and D′) germaria labeled with 1B1 (green) and anti-Vasa (red). A differentiated cyst marked by the presence of a branched fusome is outlined with a white dotted line. Scale bars represent 20 μm in (A–D). (E) Quantification of germaria, labeled with 1B1 and anti-Vasa, presenting a bam-like phenotype (accumulation of GSC-like cells containing a spectrosome), a mixed phenotype (presence of GSC-like cells and of differentiating cysts, e.g., in D), or a twin-like phenotype (lack of GSCs or lack of germ cells) in Df(3R)Exel6198, bam^Δ86/twin⁴¹, bam^Δ86 double mutant germaria in 3-, 7-, 14-, and 21-day-old females. n represents the number of germaria scored. See also Figure S4.

Figure 5

mei-P26 mRNA Is a Target of the Nos/Pum/CCR4 Complex in the GSCs (A and B) RNA immunoprecipitations (IP) with the anti-Pum antibody in bam^Δ86 ovarian extracts (left panels, Mock IP: preimmune serum) and with the anti-HA antibody in bam^Δ86 and nos-Gal4, bam^Δ86/UASp-CCR4-HA, bam^Δ86 (bam^Δ86, CCR4-HA) ovarian extracts (right panels). sop mRNA was used as a negative control. (A) Top panels show protein IP using western blots (WB). Bottom panels show the enrichment of mei-P26 mRNA in IP compared to in mock IP, visualized by RT-PCR. Inputs are protein or RNA extracts (1/10) prior to immunoprecipitation. Two (HA IP) and four (Pum IP) IPs were performed with similar results. (B) Quantification by qRT-PCR. Normalization was with sop mRNA. Quantifications were done in triplicate, and error bars represent SD. ^∗∗∗∗p < 0.0001 using the t test. (C) Schematic representation of mei-P26 3′ UTR showing position 844, the two poly(A) sites identified by RNA circularization and the three potential Pum binding motifs, including the NRE-type motif. RNA fragments tested in RNA pull-down assays (#1 to #6) and primer sets (1, 2, and 3) used to quantify the utilization of alternative poly(A) sites are also indicated. Coordinates are from the STOP codon, 1 being the first nucleotide of the 3′ UTR (see also Figure S6). (D) Quantification by qRT-PCR of ratios of mRNA levels upstream of position 844 to just upstream of poly(A) site 2, in wild-type early ovarian stages and bam^Δ86 mutant ovaries. Two primer sets (1 and 2) localized upstream of position 844 gave similar results. Means are from two independent RNA extracts quantified in triplicate, and error bars represent SD. ^∗∗∗p < 0.0005 using the t test. (E) RNA pull-down assays using the mei-P26 RNA fragments #1 to #6 shown in (C) and HA-PumC protein. Input is the in vitro synthesized protein (1/10) prior to RNA pull-down. osk and hb RNA fragments are negative and positive controls for Pum-C binding, respectively. (F) RNA pull-down competition assays of mei-P26 RNA fragment #2 with increasing amounts of osk or hb unlabeled RNA fragments. Lane 2 is HA-PumC pull-down with fragment #2 in the absence of competitor. Input is as in (E). (G) PAT assays of mei-P26 mRNA with specific primers allowing to measure potential poly(A) tails downstream of position 844 and poly(A) site 1 (left panel), and poly(A) site 2 (right panel), in wild-type and twin^DG24102 early ovarian stages. sop was used as a control mRNA. PAT assay profiles of mei-P26 poly(A) site 2, using ImageJ, are shown.

Figure 6

mei-P26 Is a Major Target of CCR4-Mediated Translational Repression for GSC Self-Renewal (A–D) Upregulation of Mei-P26 protein levels in twin, pum, and nos mutant GSCs. Wild-type (A), twin^DG24102 (B), pum^MSC/pum⁰¹⁶⁸⁸ (C), and nos¹⁸/nos⁵³ (D) germaria from 3-day-old females stained with anti-Mei-P26 antibody (green). The merges between anti-Mei-P26 (green) and 1B1 (red) are shown in (A′–D′). White arrows indicate GSCs. Scale bars represent 10 μm. (E) Quantification of fluorescence intensity ratios between GSCs and cysts in the four genotypes shown in (A–D). The numbers of germaria used in the quantification were 44 wild-type, 22 twin^DG24102, 24 pum^MSC/pum⁰¹⁶⁸⁸, and 14 nos¹⁸/nos⁵³. Error bars represent SD. ^∗p = 0.01, ^∗∗∗p = 0.0007, and ^∗∗∗∗p < 0.0001 using the t test. (F and G) Upregulation of Mei-P26 protein levels in twin mutant clonal GSCs. (F) Example of twin^DG24102 mosaic germarium labeled with GFP (green), 1B1 (purple), and anti-Mei-P26 (red) 7 days after clone induction. The white arrow indicates the twin^DG24102 clonal GSC (lack of GFP) and the white arrowhead indicates the twin^DG24102/+ heterozygous GSC. Scale bars represent 10 μm. (G) Quantification of fluorescence intensity of Mei-P26 staining in twin^DG24102/+ heterozygous and twin^DG24102 clonal GSCs. n = 8 germaria. Bars represent means with SD. ^∗∗p = 0.0088 using the t test. (H and I) Rescue of twin^DG24102 mutant phenotype of GSC loss by decreasing the gene dosage of mei-P26. twin^DG24102 (H and H′) and mei-P26^fs1/+; twin^DG24102 (I and I′) ovaries labeled with 1B1 (green) and anti-Vasa (red) in 7-day-old females. (I) The white arrows indicate GSCs; oogenesis appears normal. Scale bars represent 20 μm in (H) and 60 μm in (I). (J) Quantification of germaria containing at least one GSC in twin^DG24102, mei-P26^fs1/+; twin^DG24102 and mei-P26^mfs1/+; twin^DG24102 mutant females of 3, 7, 14 and 21 days. n represents the number of germaria scored.

Figure 7

Model for the Role of CCR4 in GSC Self-Renewal In the GSCs, the CCR4-NOT deadenylation complex interacts with Nos and Pum and is recruited to mei-P26 mRNA to repress its translation. Translational repression is counterbalanced by Vasa-mediated translational activation, leading to low levels of Mei-P26 protein, which cooperate with the miRNA pathway for silencing of mRNAs encoding differentiation factors. The CCR4-NOT complex is also likely to participate in miRNA silencing through its recruitment by GW182, as it is the case in other cell types. In cystoblasts, Bam represses nos mRNA translation (possibly together with Bgcn, Sex-Lethal, and Mei-P26; Li et al., 2013), resulting in the new association of Pum with Brat to target a different set of mRNAs (Harris et al., 2011). Mei-P26 levels do not increase, potentially due to a different mechanism of translational repression that might involve Bam. In eight-cell and 16-cell cysts, translational repression of mei-P26 mRNA is relieved, leading to an increase of Mei-P26 levels that antagonize miRNA-dependent silencing of mRNAs encoding differentiation factors.