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Targeting the autosomal Ceratitis capitata transformer gene using Cas9 or dCas9 to masculinize XX individuals without inducing mutations

Abstract

Background

Females of the Mediterranean fruit fly Ceratitis capitata (Medfly) are major agricultural pests, as they lay eggs into the fruit crops of hundreds of plant species. In Medfly, female sex determination is based on the activation of Cctransformer (Cctra). A maternal contribution of Cctra is required to activate Cctra itself in the XX embryos and to start and epigenetically maintain a Cctra positive feedback loop, by female-specific alternative splicing, leading to female development. In XY embryos, the male determining Maleness-on-the-Y gene (MoY) blocks this activation and Cctra produces male-specific transcripts encoding truncated CcTRA isoforms and male differentiation occurs.

Results

With the aim of inducing frameshift mutations in the first coding exon to disrupt both female-specific and shorter male-specific CcTRA open reading frames (ORF), we injected Cas9 ribonucleoproteins (Cas9 and single guide RNA, sgRNA) in embryos. As this approach leads to mostly monoallelic mutations, masculinization was expected only in G1 XX individuals carrying biallelic mutations, following crosses of G0 injected individuals. Surprisingly, these injections into XX-only embryos led to G0 adults that included not only XX females but also 50% of reverted fertile XX males. The G0 XX males expressed male-specific Cctra transcripts, suggesting full masculinization. Interestingly, out of six G0 XX males, four displayed the Cctra wild type sequence. This finding suggests that masculinization by Cas9-sgRNA injections was independent from its mutagenic activity. In line with this observation, embryonic targeting of Cctra in XX embryos by a dead Cas9 (enzymatically inactive, dCas9) also favoured a male-specific splicing of Cctra, in both embryos and adults.

Conclusions

Our data suggest that the establishment of Cctra female-specific autoregulation during the early embryogenesis has been repressed in XX embryos by the transient binding of the Cas9-sgRNA on the first exon of the Cctra gene. This hypothesis is supported by the observation that the shift of Cctra splicing from female to male mode is induced also by dCas9. Collectively, the present findings corroborate the idea that a transient embryonic inactivation of Cctra is sufficient for male sex determination.

Background

In the last few decades, the Mediterranean fruit fly Ceratitis capitata (Tephritidae, Medfly) has become a major invasive agricultural pest worldwide, following its spread from Africa and its globalization [1]. For the local suppression of this invasive species, alternatives to the use of pesticides are genetic control strategies. One of them is the Sterile Insect Technique (SIT), which has been applied successfully over the last six decades in various countries [2].

The prerequisites of SIT include a method to mass rear the target species in a cost-effective way and a method to sterilize them with a low impact on their fitness once released. As the released sterile females contribute to the fruit crop mechanical damage with the ovipositor and consequent infections, and the sterile males tend to mate with the released females rather than with the wild ones, it is highly preferable to develop a method of sexing and only release sterile males [3]. A number of strategies have been developed, including transgenic approaches for sexing, which allow the mass rearing of the two sexes, and sorting the males at the expanded last generation before the release. These strains can be based on the expression of a conditional female-lethal dominant gene [4] or on the transformation of genotypic female individuals into males by manipulating a gene involved in female sex determination [5]. Molecular genetics studies on Medfly sex determination have been useful for this aim, uncovering a cascade of regulatory genes widely conserved in the Tephritidae family (Fig. 1) [6,7,8,9,10]. This taxon includes many other invasive agricultural pests, such as species of the Bactrocera and Anastrepha genera [11, 12]. This fundamental knowledge is not only interesting and valuable per se [13], but also useful to develop novel sexing strategies necessary to improve the applicability of SIT. Evolutionary conservation of homologous genes and the use of transgenesis and/or CRISPR/Cas9 potentially will enable the realization of additional versatile sexing methods that can be applied in different species [8, 9, 14,15,16].

Fig. 1
figure1

Genetic pathway of sex determination in Ceratitis capitata. Cctra and Ccdoublesex (Ccdsx) pre-mRNAs exon-intron structures and sex-specific transcripts are shown. Female-specific and male-specific Cctra exons are indicated as pink and dark blue boxes, respectively. Cctra female-specific transcript on the left contains a 429 aa long ORF. Cctra male-specific exons introduce premature stop codons in male-specific longer transcripts (orange vertical bars). CcTRA M1 and M2 male-specific isoforms contain truncated CcTRA ORFs represented by azul regions. In XX embryos, maternal CcTRA (orange circle) and CcTRA-2 (green circle) proteins promote female-specific splicing of newly transcribed Cctra pre-mRNA, suppressing male-specific splicing by binding to TRA/TRA-2 cis regulatory elements (red spots). Female-specific Cctra mRNA encodes zygotic CcTRA (violet circle) that maintains (together with zygotic CcTRA-2; dark green circle) the Cctra autoregulation induced by the maternal contributions by a feedback loop. Both CcTRA and CcTRA-2 proteins promote also female-specific splicing of the downstream Ccdsx pre-mRNA, producing mRNAs that include a female-specific exon (pink) and encode CcDSXF isoform inducing female sexual differentiation [6]. In XY embryos the Y-linked Maleness-on-the-Y gene (MoY) induces male-specific Cctra splicing and, hence, the collapse of the positive feedback loop [7]. By default, male-specific splicing of Ccdsx leads to male-specific splicing and CcDSM isoform inducing male sexual differentiation [6, 8]

The sex determination of Medfly is based, as in Drosophila melanogaster, on sex-specific alternative splicing of key regulatory genes, including transformer (tra), transformer-2 (tra-2) and doublesex (dsx) orthologues (Fig. 1) [6, 7, 17,18,19,20]. Cctra is a sex determining genetic switch, which is set to ON in XX embryos and to OFF in XY embryos during a narrow temporal window at 5–6 h from oviposition [8]. In contrast to Drosophila, in XX Medfly embryos, Cctra and the auxiliary Cctransformer-2 (Cctra-2) maternal mRNAs are also required to establish a stable activation of Cctra by female-specific splicing which relies on a positive feedback loop [6, 19]. The female-specific Cctra mRNA encodes a full-length 429 aa protein arising from the translation of an evolutionarily conserved ORF contained in the first, fourth and fifth exons (Fig. 1). In males, two longer alternative Cctra RNA isoforms, containing all five exons, encode for two truncated CcTRA proteins called CcTRA M1 (59 aa) and CcTRA M2 (99 aa) (Fig. 1). Embryonic transient RNA interference targeting mRNAs of either genes led to XX males, which are fertile even in the absence of the Y chromosome [6, 19]. As in Drosophila, Cctra and Cctra-2 are required for the female-specific splicing of Ccdoublesex (Ccdsx). The observation that some XX individuals are transformed in gynandromorphs (showing male-specific antennae and ovipositor or no antennae and male gonads) suggests that sex determination is cell-autonomous, as in Drosophila [6]. A TRA/TRA-2 binding element (13 nt long) is present in multiple copies in the Ccdsx female-specific exon, permitting a positive regulation by CcTRA/CcTRA-2, which leads to the use of this exon in Ccdsx transcripts of XX individuals, similarly to Drosophila [7, 18]. In contrast to Drosophila, multiple copies of this splicing regulatory element are also present in Cctra locus, within and in proximity to the male-specific exons. In this other novel case, these cis elements mediate, by CcTRA/CcTRA-2 binding, exon skipping in XX individuals leading to CcTRA-encoding female-specific mRNAs [6]. In XY embryos, Maleness-on-the-Y (MoY) encodes a novel short protein, MOY, of still unknown biochemical function, that leads, either directly or indirectly, to male-specific splicing of Cctra and exons inclusion, at 5–6 h from oviposition [8]. The presence of male-specific exons introducing stop codons in the 429 aa long Cctra ORF leads to two major RNAs encoding truncated polypeptides (respectively 59 and 99 aa long) and hence considered to be non-functional [6].

We planned to experimentally confirm this deduction, by Cas9-induced mutations in the Cctra, which would impact both the male- and female-specific ORFs. Furthermore, the availability of an efficient single RNA to induce mutations in a female-determining gene would open the future possibility to develop a gene drive strategy aimed at manipulating the sex ratio and hence the reproduction rate of this harmful species [4]. CRISPR/Cas9 has been used in the Medfly genome to target autosomal genes having two copies for each cell [16, 21, 22]. After targeting the white eye Medfly gene by injecting into early embryos in vitro pre-assembled and solubilized Cas9 ribonucleoprotein complexes (RNPs), containing sgRNA, adults showed partial mutant phenotypes caused by somatic mosaicism [16]. The most extreme mutant phenotype consisted of a fly mosaic with one of the two eyes fully colorless. While biallelic mutations were observed only in somatic clones of the fly, the germ line transmission rate was very high, reaching 100% in one case. On the contrary, targeting a Medfly single copy gene, as the Y-linked MoY, in XY individuals by Cas9 ribonucleoproteins injections, 70% of mutant G0 individuals showed intersexual phenotype and 30% were transformed into XY mutant G0 females [8].

We reasoned that introducing loss-of-function frameshift mutations in the first Cctra exon with CRISPR/Cas9 would lead to mutant alleles coding for truncated CcTRA proteins. The expected truncations would affect not only the 429 aa long female-specific ORF, but also the carboxy-terminal ends of two male-specific 59 and 99 aa ORFs. A masculinization of XX individuals by permanent loss-of-function mutations of Cctra altering also the male-specific CcTRA polypeptides would support the previous suggestion that these products are indeed non-functional.

Since in Drosophila tra and tra-2 mutant alleles are recessive, we reasoned that also in the Medfly the presence in the same cell and in its clonal descendants of only monoallelic indel (insertion/deletion) mutations in Cctra (+/− heterozygous state) would be insufficient to masculinize XX cells. Thus, in the somatic mutant clones of these XX individuals, the CcTRA protein expressed from the wild-type allele would lead to female-specific splicing of Cctra pre-mRNAs from both wild-type and mutant alleles, leading to female sexual phenotype. Hence, only biallelic loss-of-function Cctra mutations (Fig. 2; Cctra1−/Cctra2−) in the same XX cell and its cellular descendants would lead to a male-specific Cctra and the downstream Ccdsx RNAs, causing a partial (mosaicism) or full (very early and high bi-allelic mutagenesis) masculinization of XX adults.

Fig. 2
figure2

Experimental design to produce G1 XX males bearing heteroallelic mutation of Cctra. Two sets of parallel Cas9-RNP injections to target Cctra into XX embryos can lead to both G0 XX males and XX females. The G0 adults from the two sets can bear some Cctra monoallelic independent mutations (mosaicism) both in the soma and in the germ line. In set n. 1, the injection mix contains also Cctra-dsRNA to induce full masculinization of XX embryos (Pane et al., 2002). Hence, the G0 XX males from set n. 1 can be crossed with G0 XX females from set n. 2, to produce a G1 XX progeny, expected to be composed mostly of XX females (carrying either none or monoallelic mutations) and of few G1 XX males, carrying heteroallelic mutations of Cctra (Cctra1−/Cctra2−) inherited from the respective parents

Results

Cas9-RNP injections targeting Cctra lead to fully masculinized XX flies in the G0 progeny

With the aim of inducing indels leading to frameshift mutations in Cctra, we used Cas9 RNPs injections as a delivery method. In particular, a CRISPR/Cas9 Cctra target site was chosen within the coding region of exon 1 on the antisense strand to design a single guide RNA, named sgtraEx1 (Additional file 1: Fig. S1A). The targeted 20 bp long sequence is about 20 bp upstream of the first donor splicing site and upstream to the female-specific long open reading frame encoding the CcTRA protein (Additional file 1: Fig. S1B). As described above, previous literature data showed that Cas9 RNPs applied to Medfly embryos led to a relatively low somatic biallelic mutation rate overall but a high rate in the germ line [16]. Based on this study, we speculated to observe masculinization of XX Cctra mutant individuals only at G1 after crossing G0 XY males and G0 XX females developed from Cas9-injected. However, the discrimination of rare Cctra1−/Cctra2− heteroallelic mutant XX males among the 50% of the G1 progeny being XY males would have been tedious and challenging. We simplified their identification by planning to detect them among a G1 female-only XX progeny, obtained crossing XX males and females obtained from RNP-injected embryos (Fig. 2). Among these G1 XX females, Cctra-1−/Cctra2− XX males would be easily detected even if very few, with the respect of the majority of XX females carrying either none or only one Cctra mutant allele (Fig. 2).

To produce a larger number of XX males (Fig. 2, set 1), from Cas9-injected XX embryos, a mix of Cas9-sgtraEx1 RNP and Cctra dsRNA, to efficiently masculinize XX, was injected into 370 XX embryos (Table 1, set n. 1). The aim was to obtain XX fertile males potentially carrying Cas9-induced Cctra monoallelic mutations also in the germ line. However, no pupae and adult flies emerged from this set of injections. When Cas9-sgtraEx1 RNP alone targeting Cctra were delivered into 400 XX embryos, few adults developed (3%; 12/400) (Table 1, set n. 2). It is likely that the co-presence of dsRNA+Cas9/sgRNA molecules could have a combined higher lethal effect for unclear reasons. Injections of dsRNA-Cctra alone resulted in 78 adults out of 200 XX embryos injected, with 73 XX being masculinized individuals and 5 being intersexes (Table 1, set n. 3). A similar survival rate was obtained when we injected sgtraEx1 RNA molecules but no effect (1 μg/μL), at a 5 times higher concentration being more susceptible to RNA degradation (70 females out of 160 injected embryos; Table 1, set n. 4).

Table 1 XX-only embryonic injection sets

Although upon Cas9-sgtraEx1 RNP injections we observed a very limited survival rate, the XX adults displayed some interesting features (Table 1, set n. 2). Indeed, the G0 progeny was composed not only of six unaffected females, as we expected (Fig. 2 set 2), but also six XX males. These findings are suggestive of an unusually high rate of biallelic mutations. It is also worth noting that no intersexes were observed, suggesting an all-or-none effect on Cctra female-specific function of the Cas9 + sgtraEx1 injection.

Considering the apparently high efficiency of the ribonucleoprotein injections in set n. 2 (Table 1) in masculinizing 50% of the G0 XX individuals, we reasoned that 1) also the XX females contained at least some somatic clones bearing monoallelic Cctra mutations, though with no phenotypic effect, and that 2) a high mutagenic rate could also be present in the germ lines of these XX female adults as in the XX males. Assuming a 20–50% transmission rate of mutant alleles for each G0 parent to the next progeny as previously observed in the Medfly [16], the probability to observe a double mutant individual in the G1 progeny (Fig. 2) would be in a range of 4–25%. When we crossed among them the six XX males and six XX females from injection set n. 2 (Table 1), all 100 individuals of G1 were females, indicating that the six XX masculinized fathers were fertile. However, the absence of XX males in the G1 progeny indicated that, if any Cctra mutation was induced by Cas9 in the parental germ lines (male and female ones), the transmission rate was lower than 10% for each parent as the expected G1 heteroallelic mutants frequency would be less than 1% of the progeny (hence not detectable among a number of 100 individuals).

Lack of indels in the targeted Cctra region in most cDNA clones from XX G0 males and in all genomic DNA clones from G0 XX females

The six females and six XX males, which composed the G0 progeny of set n. 2, were analyzed respectively by RT-PCR and genomic PCR, to investigate Cctra splicing and DNA sequence of the targeted site.

The six reverted XX G0 males showed only male-specific Cctra transcripts, as expected for adult flies having a full fertile male phenotype (Fig. 3). These data, together with the absence of female-specific Cctra mRNAs in all six males, suggested the presence of biallelic mutations in most, if not all, of the somatic cells of these XX G0 males. Shotgun plasmid cloning of the RT-PCR reactions from the six XX G0 males, followed by PCR colony screening of 30 clones (five colonies A-E, for each of the six XX males) led us to arbitrarily select 13 clones for sequencing (two or three cDNA clones for each male) (Additional file 1: Figure S2 and Figure S3)(Additional file 2). The splicing isoforms detected in the six XX males corresponded mostly to the know M1 and M2 Cctra male-specific isoforms. Out of 13 cDNA clones from the six XX males, seven correspond to male-specific Cctra isoform M1 (59 aa), two correspond to the male-specific isoform M2 (99 aa), one to a new splicing male-specific isoform (Male 1D encoding a 44 aa long protein isoform, named M3), one to the female-specific isoform (429 aa) and one to an unspliced longer isoform (male 5C) (Additional file 1: Figure S3; Additional file 2) [6]. Very surprisingly, despite the observed Cctra male-specific full shift, 11 cDNA clones showed only wild-type sequences (Additional file 1: Figure S3). In one XX male, we have found a cDNA showing a 16 bp long deletion (cDNA 3E), in addition to a wild type cDNA clone (cDNA 3B) (Additional file 1: Figure S1D). The mutated cDNA encodes a 35 aa long CcTRA truncated protein. Another XX male contained two wild type (5B and 5D) cDNA clones and a mutated one lacking of 5 bp (5C) (Additional file 1: Figure S1C). This cDNA Male 5C encoded a truncated CcTRA protein of only 42 aa (Additional file 1: Figure S1C). The male 5C cDNA from unspliced Cctra RNA seems to correspond to a previously described RNA only present in adult females [6]. The female specificity of this unspliced product could be due to the binding of female-specific CcTRA/CcTRA-2 complex to the Cctra pre-mRNA required for the autoregulation. Interestingly, the Cctra unspliced isoform we found in one XX male contains also the Cas9-induced 5 bp deletion. We speculated that the 5 bp long deleted region of Cctra could be involved in enhancing the recognition of the 5′ donor site, which is only 20 bp downstream to the deletion by the spliceosome. We have found that these 5 bp are perfectly conserved in other Tephritidae tra orthologues, suggesting their requirement for proper Cctra male-specific default splicing (Additional file 1: Figure S1E). On the other hand, the cDNA 3E containing even a larger deletion (16 bp) of the same Cctra region performed a male-specific splicing, indicating that this sequence (14 bp out of 20 bp targeted sequence conserved in 5 distantly related Tephritidae species; Additional file 1: Figure S1E) is not strictly required to perform this alternative splicing but could be involved in performing the female-specific one. Collectively, these data showed intriguingly that the six XX males had a full switch from female-specific to male-specific splicing of Cctra, even in the presence of a very low (hence, mostly monoallelic) or even zero number of mutant Cctra alleles.

Fig. 3
figure3

RT-PCR analysis of reverted XX males. (A) The six XX males from injection set n. 2 (Table 1) showed only male-specific Cctra transcripts (500 bp) and shorter less abundant splicing variants. No traces of female-specific transcripts were visible in the gel electrophoresis (160 bp) (B) RT-PCR with MoY-specific primers indirectly confirmed the absence of the Y chromosome in these six fully reverted XX males and its presence in XY flies (positive control)

As the six XX females showed a normal female phenotype, female-specific Cctra splicing was expected to be found, even if they were carrying monoallelic Cctra mutations (Fig. 2). Hence, Cctra genomic DNA (rather than RNA or cDNA) was analyzed and eight plasmid clones showed only Cctra wild-type sequences (Additional file 1: Figure S4; Additional file 3). The lack of Cctra mutations in the DNA clones from all six G0 females and in most of the cDNA from the six XX males is consistent with the absence of XX mutant heteroallelic Cctra− 1/Cctra− 2 males we observed in their G1 progeny.

Embryos co-injections of dCas9 and sgtraEx1 lead to partially masculinized XX embryos and adult flies, indicating a long-lasting effect in the absence of mutations

We speculated that this Cas9 ribonucleoprotein complex was able to bind but not efficiently cut the Cctra DNA target site. The dead Cas9 (dCas9) is a mutant Cas9 which lacks of only the endonuclease activity and it can be used to perform transient transcriptional repression, named CRISPR interference, or iCRISPR [23,24,25]. We co-injected the sgRNA sgtraEx1 (1 μg/μl) with a plasmid bearing a dCas9 transgene under a Drosophila actin promoter, expecting that dCas9 would be produced after transcription and translation and would bind the available sgRNA [24] (Table 1, set n. 5). A higher concentration of sgRNA (1 μg/μl; see mat. & meth.) was used in the injected mix because we expected that these RNA molecules being not pre-assembled with Cas9 before injections, could have been more exposed to degradation. This high concentration of sgRNA alone had no effect on Cctra female-specific splicing in injected XX embryos and in developed XX adults (Table 1, set n. 10; Fig. 4, B). Three out of ten XX adult females showed malformations of the gonadal apparatus, which suggested a mild masculinization effect (Additional file 1: Figure S5A). RT-PCR analysis of Cctra on RNA from these three XX adult flies confirmed the presence of also male-specific RNAs, indicating that the ovipositor malformations are likely the result of a partial masculinization during development (Additional file 1: Figure S5B). These data indicated that the dCas9 can induce a partial masculinization of XX embryos and a stable shift toward male-specific splicing of Cctra likely in some somatic clones.

Fig. 4
figure4

Molecular partial masculinization of XX embryos by dCas9 targeting Cctra. (A) RT-PCR analysis of Cctra sex-specific transcripts in 15 h old XX embryos, following injections of various samples (Table 1, set n. 6–8) at 1 h after egg laying (Panel 1). The XX embryos were injected respectively with Cas9 protein+sgtraEx1 (first lane), with sgtraEx1 + Cas9-encoding plasmid (pIE1-Cas9; second lane) and with dCas9-encoding plasmid (pAct-dCas9) (third lane). Male-specific Cctra transcripts were detected (500 bp cDNA fragment) in all three samples of injected XX embryos, in addition to the female-specific transcripts (160 bp cDNA fragment). RT-PCR analysis of the Y-linked MoY gene indirectly confirmed the absence of Y chromosome in all 3 samples and in XX females, and its presence in a mixed XX/XY embryos sample and in adult XY flies (Panel 2). CcSOD positive control is shown in panel 3. (B) Negative controls. RT-PCR of Cctra sex-specific transcripts in 15 h old XX embryos, following injections at 1 h after egg laying (Table 1, set n. 9–13). The XX embryos were injected respectively with Cas9 protein, Cas9-encoding plasmid, dCas9-encoding plasmid, with sgtraEx1 and with buffer alone. Only female-specific Cctra transcripts were detected (160 bp) in all samples of injected XX embryos (Panel 1). In Panel 2 and 3, the control of the karyotype and positive controls, conducted as in A, are shown

We investigated the sex-specific splicing pattern of Cctra in XX-only embryos, injected at 1 h after egg laying, and developed for additional 14 h (set n. 6–13). Injections of Cas9 recombinant protein+sgtraEx1 RNP (set n. 6), or co-injections of sgtraEx1 with plasmids encoding either Cas9 (driven by E1 early promoter [23]) or dCas9 (set n. 7 and set n. 8) led to the appearance of additional male-specific Cctra transcripts (Table 1, Fig. 4A). Injections of only buffer, sgtraEx1, Cas9 protein, Cas9-encoding and dCas9-encoding plasmids had no effect (Fig. 4B). These data suggest that, as Cas9, also dCas9 can induce male-specific splicing of Cctra during the first hours of development. Hence, no Cctra mutations are required for this splicing change.

Discussion

The Cas9-sgtraEx1 RNPs injected into XX Medfly embryos led to a masculinization of 50% of XX individuals. All six XX males showed by RT-PCR and cDNA sequencing analyses mostly male-specific Cctra isoforms, concordant with the observed male phenotype. Unexpectedly, no indel mutations were detected in cDNA fragments from the Cas9 targeted site in four out of six males. Two XX males showed a mix of wild type and mutated cDNA fragments, suggesting the presence of monoallelic mutations in some cellular regions. XX males and XX females from injected embryos produced a G1 consisting of only XX females, which indicated absence of homozygous individuals for mutant Cctra alleles. We concluded that very low mutation rate, if any, was reached not only in the soma but also in the germ line of injected G0 individuals. In contrast, Meccariello et al. [16], observed that mutant mosaic G0 flies mutagenized by Cas9 in the white-eye gene transmitted germ line mutations to the progeny at a very high rate (up to 100%). Hence, the Cas9-sgtraEx1 is likely very inefficient in mediating Cas9 gene disruption but surprisingly very efficient in masculinizing XX individuals. These data suggested that the Cas9 ribonucleoprotein promoted masculinization by inducing male-specific Cctra splicing in 50% of XX embryos which developed into adults by a mechanism different than gene disruption.

We reasoned that the sgRNA designed for the CRISPR experiment and/or the Cctra targeted region structural features posed limitations in the second step of the Cas9 action, namely the endonuclease activity, but not in the first step, the binding to the Cctra genetic locus. Indeed, a two-state model for Cas9 binding and cleavage was recently proposed: a seed match triggers binding but only extensive pairing with target DNA leads to cleavage [26]. Target sequence mismatches can induce the Cas9-RNP complex to bind also off-target sites without DNA cleavage, because the transition to the active conformation is prevented [26, 27]. Co-injections of sgtraEx1 and a plasmid encoding dCas9 into XX embryos induced a partial shift of Cctra splicing toward male-specific pattern after few hours of development and the development of XX females (three out of ten) with malformed ovipositor. These females were found to be molecular intersexes, as they showed both female-specific and male-specific Cctra isoforms. Also, these malformed females showed a mix of male and female-specific Cctra transcripts and, hence, correspond to partially masculinized individuals (intersexes) [6]. Similar malformed ovipositors were observed by Pane et al. [6] following embryonic RNA against Cctra. The lack of fully masculinized XX individuals in the progeny of ten individuals suggests a reduced efficiency of dCas9 in masculinizing XX individuals. However, this could be due to the different delivery methods of Cas9 and dCas9. In the first case, purified recombinant Cas9 ready to act was injected, while in the second case a dCas9 encoding transgene was transcribed from a Drosophila actin promoter, after embryos injections of a plasmid. Lower efficiency is to be expected in the second delivery method, due to the transcription and translation steps required to express dCas9. The transient binding of Cas9 RNPs to the 5′ Cctra DNA region could have reduced the Cctra zygotic transcription during the first hours of embryogenesis and, hence, the accumulation of female specifically spliced Cctra mRNA, promoted by the maternal Cctra contribution in XX embryos. This transient reduction of newly transcribed Cctra female-specific mRNA and of the encoded CcTRA protein in the XX embryos could have blocked the establishment of Cctra female-specific autoregulation leading to a negative epigenetic effect on Cctra. Similarly, a transient depletion of Cctra mRNA by embryonic RNAi led to a collapse of its positive autoregulation and to obtain XX fertile males expressing male-specific Cctra RNAs [6].

Conclusions

The question if CcTRA male-specific ORFs are required for male-specific Cctra splicing remains still open, as biallelic Cctra mutant XX males were not obtained. The second question if the chosen sgtraEx1 guide RNA is suitable for future gene drive strategy aimed to efficient mutagenesis by Cas9 had a conclusive and negative reply, as very low mutagenesis rate was observed. However, these data support the hypothesis that the transient binding of the Cas9-sgtraEx1 ribonucleoprotein complex on the first Cctra exon during the first hours of embryogenesis led to a repression of the establishment of the Cctra female-specific autoregulation in XX embryos even in the absence of induced mutations. Our study raises new general issues concerning the use of CRISPR/Cas9 method. We serendipitously uncovered a novel problem of unplanned stable changes in the expression of genes able to autoregulate, which calls for further investigation. If a Cas9 + sgRNA binds to off target sequences of autoregulating bistable genes, this event can provoke long lasting epigenetic effects even in the absence of DNA mutations.

Methods

Rearing of Ceratitis capitata

Wild type (WT) and transgenic Medfly lines were maintained under standard rearing conditions. The WT Benakeion strain, which has been reared in laboratories for more than 20 years, was obtained from P. A. Mourikis 30 years ago (Benakeion Institute of Phytopathology, Athens, Greece). The strains were reared in standard laboratory conditions at 25 °C, 70% relative humidity and 12:12 h light–dark regimen. Adult flies were fed yeast/sucrose powder (1:2).

RNP complex assembly and injections

Cas9 was expressed as his-tagged protein and purified from bacteria [16, 19]. sgRNA was designed using the CHOPCHOP online software [28]. The lack of SNPs within this 20 nt long sequence in three different Ceratitis lines (Benakeion, used in this study, ISPRA [22] and FAM18 Ceratitis [8]) suggested that no Cas9-resistant Cctra alleles would be already present in individuals of these lab strains. Template for sgRNA in vitro transcription were generated by annealing two complementary oligonucleotides (PAGE-purified, Life Technologies) as previously described [16, 21], using the primers F-sgtraEx1 and Reverse-Crispr from Life Technologies (Additional file 4). sgRNA was synthesized according to instructions of the Megascript® T7 kit (Ambion) with 1 μg of DNA template and a 5′ flanking T7 promoter. After RNA synthesis, the template was removed by incubating with TurboDNase® (Ambion) for 15 min at 37°. Prior to the injection, the RNP complex was prepared by mixing 1.8 μg/μL of purified Cas9 protein with approximately 200 ng/μL of sgtraEx1, containing 300 mM KCl [16]. The mix was incubated for 10 min at 37 °C. A glass needle was filled with the pre-loaded sgtraEx1-Cas9 mix and the injection was performed into the posterior end of embryos collected 45 min after egg laying as described for RNA interference in Ceratitis capitata [6]. When injecting sgRNA alone, a 5 times higher concentration (1 μg/μL) was used in the injected mix, because we expected that these RNA molecules, being not pre-assembled with Cas9 before injections, could have been more exposed to degradation.

RNAi and XX-only progeny production

A Cctra cDNA 800 bp long fragment was PCR amplified using RNA from female adults of C. capitata and longer 164+/900- primers, introducing a T7 promoter sequence at each extremity. In vitro transcription of Cctra dsRNA was performed using the Ambion MEGAscript® RNAi kit T7 RNA polymerase, following manufacturer instructions. Embryonic RNAi (0.5 μg/μL dsRNA solution) was used to repress Cctra in XX/XY embryos and to produce male only progeny. Single males from this progeny were crossed with three females in small cages and the crosses having XX males were identify by Y-specific PCR (Y-specific primers) [8] on a small sample of laid embryos.

dCas9 encoding plasmid and injections

Plasmid expressing dCas9 under the control of the Drosophila melanogaster actin promoter was kindly provided to GS by Lenny Rabinow (Perrimon’s lab, Harvard, USA) [23]. A mix containing 1 μg/μL of pAct-dCas9 plasmid and 1 μg/μL of sgtraEx1 transcribed in vitro into the posterior end of embryos. We used 5 times higher concentration of sgRNA because we expected that these small RNA molecules being not pre-assembled with Cas9 before injections, could have been more exposed to degradation.

RNA extraction and RT-PCR

Total RNA was extracted from pools of embryos, intersexes, male and female adults using TRIzol® Reagent (Invitrogen®) following manufacturer instructions. Oligo-dT-primed cDNA was prepared from DNAse-treated total RNA using EuroScript® m-MLV reverse transcriptase (Euroclone®). RT-PCR expression analysis was performed with the following primers: Cctra 164+/320-, CcSOD+/CcSOD- and CcMoY A+/CcMoY A- (Additional file 4). For XX malformed females obtained from XX only embryos with dCas9 and sgtraEx1 Cctra RT-PCR was performed using Cctra 164+/900- primers pair, annealing on the same exon as Cctra 320- primer (Additional file 4). Gel electrophoresis diagnostic amplicon run was performed using Marker III (Lambda genomic DNA digested with EcoRI/HindIII) or 100 bp ladder from Thermo Scientific®.

DNA extraction and molecular analysis

DNA extraction was performed, with minor modifications, according to the protocol of Holmes and Bonner et al. [29]. Adult XX female flies G0 were placed in a 1.5 ml tube and manually crushed with a pestle in 200 ml Holmes Bonner buffer (Urea 7 M, 281 Tris-HCl 100 mM pH 8.0, EDTA 10 mM pH 8.0, NaCl 350 mM, SDS 2%). Subsequently, DNA was purified by phenol/chloroform extraction, followed by chloroform extraction and ethanol precipitation. The pellet was resuspended in 30 μl water containing RNase A.

cDNA and gDNA cloning and sequencing

PCR cDNA fragments from XX adult males were cloned into pGEM-T Easy Promega® vector according manufacturer instruction. PCR colony screening was carried out using 164+ and 320- primers. Positive colonies were used to extract plasmid DNA which was sequenced using Applied Biosystem® Big Dye v 3.1. Genomic DNA from the six G0 XX females was used as template to amplify the region encompassing the target sites, using the primers Cctra 164+ and Cctra 164-Rev (Additional file 4). DreamTaq (Life Technologies) polymerase was used for PCR amplifications according to the manufacturer’s instructions. The PCR products were purified with StrataPrep PCR Purification Kit (Agilent Technologies) and subcloned using StrataClone PCR cloning Kit (Agilent Technologies). Positive clones were sequenced by Sanger method and ABI 310 Automated Sequencer (Applied Biosystems) using the primer Cctra 164+ (Additional file 4).

RNA extraction from injected embryos after 15 h of development

The pools of 40 embryos injected with various mixes (Table 1) were let develop for 15 h at 25 °C, 70% relative humidity. The embryos were then detached from the cover slip using heptane, which dissolves the glue, and collected in a 1.5 mL tube. They were then washed three times with 1X PBS to remove heptane before RNA extraction was performed using TRIzol® Reagent (Invitrogen®) following manufacturer instructions. The RNA samples were analyzed for Cctra splicing pattern by RT-PCR using the primers Cctra 164+ and Cctra 900- (Additional file 4).). The cDNA and genomic sequences were deposited at the GenBank database with the following accession numbers: MW200161 to MW200180.

Availability of data and materials

The cDNA and genomic sequences were deposited at the GenBank database with the following accession numbers: MW200161 to MW200180.

Abbreviations

SIT :

Sterile Insect Technique

ORF :

Open Reading Frame

CRISPR :

Clustered Regulated InterSpaced Palindromic Repeats

RNP :

Ribo-Nucleo-Proteic Complex

dsRNA :

double strand RNA

sgRNA :

single guide RNA

iCRISPR :

interference CRISPR

dCas9 :

dead Cas9

SNP :

Single Nucleotide Polymorphism

RNAi :

RNA interference

WT :

Wild-Type

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Acknowledgements

We would like to thank Lenny Rabinow (Harvard University, USA) for providing dCas9 plasmid vector and Donald L. Jarvis (University of Wyoming, USA) for providing E1-P-Cas9. GSA and AM initiated the project. We wish to thank Luigi Vitagliano (IBB-CNR, Italy) for in depth discussion, insights and manuscript reviewing. This study was benefited from discussions at International Atomic Energy Agency funded meetings for the Coordinated Research Project “Comparing Rearing Efficiency and Competitiveness of Sterile Male Strains Produced by Genetic, Transgenic or Symbiont-based Technologies”. We thank the anonymous reviewers and the guest editor for their helpful and generous suggestions to improve the description of this study.

About this supplement

This article has been published as part of BMC Genetics Volume 21 Supplement 2, 2020: Comparing rearing efficiency and competitiveness of sterile male strains produced by genetic, transgenic or symbiont-based technologies. The full contents of the supplement are available online at https://bmcgenet.biomedcentral.com/articles/supplements/volume-21-supplement-2.

Funding

The PhD Biology program at University of Naples Federico II supported this study with fellowships to AM and PP. The Department of Biology supported this study with small-budget grants (Ricerca Dipartimentale) to GSA, SA and MS, for data collection and their interpretation. MDR acknowledges support from the UZH University Research Priority Program Evolution in Action.

Publication costs are funded by the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA (CRP No.: D4.20.16) Vienna, Austria. The funding bodies provided the financial means to allow the authors to carry out the study and the funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

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AM, AG, MGI, GDC, performed set n. 1–4 embryonic injections (Table 1) and the embryonic injections of Cctra dsRNA+Cas9 + sgtraEx1, which led to 100% lethality. PP performed PCR, cloning and sequencing analyses of the 6 XX males and 6 XX females from of injection set n. 2 (Table 1). PP and GSO performed injection set n. 5 and RT-PCR of the 3 XX malformed females. PP and GV performed injection set n. 6–9 and GV performed RT-PCR analyses on the 15 h-old injected embryos. PP performed the cross of G0 males and females from set n. 2 and visually screened the G1 progeny. AM, PP, AG, MGI, GDC, GSO and GV maintained the Medfly strains, preparing larval and adult food, performing crosses and collecting embryos. GSA wrote the paper, with the inputs of MDR, SA, MS, and AM. GS prepared the figures, with contributions of AM, MS and PP. All authors contributed with minor corrections/editing of the manuscript, especially AG. All the authors have read and approved the final version of the manuscript.

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Correspondence to Giuseppe Saccone.

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Primo, P., Meccariello, A., Inghilterra, M.G. et al. Targeting the autosomal Ceratitis capitata transformer gene using Cas9 or dCas9 to masculinize XX individuals without inducing mutations. BMC Genet 21, 150 (2020). https://doi.org/10.1186/s12863-020-00941-4

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Keywords

  • iCRISPR
  • Sex determination
  • Ceratitis capitata
  • Epigenetics
  • Autoregulation
  • Transformer