Sense organs acquire their distinctive shapes concomitantly with the differentiation of sensory cells and neurons necessary for their function. Although our understanding of the mechanisms controlling morphogenesis and neurogenesis in these structures has grown, how these processes are coordinated remains largely unexplored. Neurogenesis in the zebrafish olfactory epithelium requires the bHLH proneural transcription factor Neurogenin 1 (Neurog1). To address whether Neurog1 also controls morphogenesis, we analysed the migratory behaviour of early olfactory neural progenitors in neurog1 mutant embryos. Our results indicate that the oriented movements of these progenitors are disrupted in this context. Morphogenesis is similarly affected by mutations in the chemokine receptor gene, cxcr4b, suggesting it is a potential Neurog1 target gene. We find that Neurog1 directly regulates cxcr4b through an E-box cluster located just upstream of the cxcr4b transcription start site. Our results suggest that proneural transcription factors, such as Neurog1, directly couple distinct aspects of nervous system development.

The morphology of sense organs of the head is exquisitely adapted for detecting specific stimuli. At the same time that morphogenetic movements sculpt these structures during development, cell types are specified that will participate in their function either by detecting specific stimuli or transmitting sensory information to the brain. There is a growing literature concerning the molecular mechanisms controlling morphogenesis and specification of different cell types in sensory organs. Whether morphogenesis and cell fate specification are linked molecularly during the development of these organs, on the other hand, is unclear.

The zebrafish olfactory epithelium develops from a horseshoe-shaped pool of neural progenitors located at the boundary between the anterior neural plate and flanking non-neural ectoderm (Miyasaka et al., 2013). Neurogenesis in this system occurs in two distinct waves (Madelaine et al., 2011). Between 10 and 24 h post-fertilisation (hpf), a set of early-born olfactory neurons (EON) differentiates. These neurons act as pioneers during the establishment of projections of olfactory sensory neurons (OSN) to the olfactory bulb, which are born during the second wave. Once OSN projections are established, a subset of EON dies by apoptosis (Whitlock and Westerfield, 1998). The development of both EON and OSN require the partially redundant function of the basic helix-loop-helix (bHLH) proneural transcription factors Neurog1 and Neurod4 (Madelaine et al., 2011).

Concomitant with the earliest wave of neurogenesis in the developing olfactory epithelium, morphogenetic movements shape olfactory progenitors and newly born EON into a placode (12-18 hpf) and then a rudimentary cup (18-24 hpf) (Whitlock and Westerfield, 2000; Miyasaka et al., 2007; Breau et al., 2017). This process requires the chemokine receptor Cxcr4b, and its ligand Cxcl12a. Interfering with the activity of this signalling pathway, either by mis-expression of Cxcl12a or in odysseus (ody) embryos that carry mutations in cxcr4b, affects olfactory placode morphogenesis (Miyasaka et al., 2007).

In parallel to its role in olfactory neurogenesis, Neurog1 is ideally placed to control the cell movements that underlie morphogenesis of the olfactory cup, thus coupling morphogenesis and neurogenesis. Consistent with this idea, we find that the early phase of morphogenesis is compromised in neurog1 mutant embryos. We provide evidence that the underlying defect is a lack of cxcr4b expression, which is directly regulated by Neurog1. Thus, we have uncovered a parsimonious mechanism for coordinating multiple features of peripheral sensory organ development.

To address a potential role for Neurog1 in the morphogenesis of the peripheral olfactory organ, we analysed its formation by time-lapse imaging neurog1 mutant or control embryos carrying a Tg(-8.4neurog1:gfp) transgene (Golling et al., 2002; Blader et al., 2003); this transgene recapitulates the expression of endogenous neurog1 during the development of the olfactory epithelium and has already been used as a short-term lineage label for the progenitors of EON (Madelaine et al., 2011; Breau et al., 2017). As recently described by Breau and colleagues, we found that EON reach their final position in control embryos by converging towards a point close to the centre of the future cup (as represented in Fig. 1A; Breau et al., 2017). Considering overall antero-posterior (AP) length of the EON population, this convergence appears to happen quickly until the olfactory placode has formed (12-18 hpf), after which it slows (Fig. S1A,B; Movie 1). In neurog1hi1059 mutants, we observed a delay in convergence, which translates into a longer AP length spread of EON than seen in control embryos (Fig. S1B). This delay is overcome, however, with the olfactory cup in neurog1hi1059 mutant embryos ultimately attaining AP length of control embryos (Fig. S1B).

Fig. 1.

Oriented cell movements are affected in neurog1hi1059 mutant embryos during olfactory cup formation. (A) Graphic representation of the morphogenesis of olfactory cup from 12 hpf to 27 hpf, showing a dorsal view of the three olfactory stages: olfactory territory (12 hpf), olfactory placode (18 hpf) and olfactory cup (24 hpf). EON progenitors are represented in green as visualised with the Tg(-8.4neurog1:gfp) transgene. At 12 hpf, the −8.4neurog1:GFP+ placodal domain can be divided into anterior, middle and posterior regions. The early (12-18 hpf; black) and late (18-27 hpf; grey) phases of morphogenesis are noted in the time line. (B) Tracks showing migration of EON of control (black) or neurog1hi1059 mutant (magenta) embryos. Twelve tracks are represented (two cells each from the left and right of three embryos) for each of the anterior, middle and posterior domains of the developing cup indicated in A. The origin of the tracks has been arbitrarily set to the intersection of the x/y-axes and the early (coloured) and late (grey) phases of migration have been highlighted. (C) Mean tracks for anterior EON of control (black) or neurog1hi1059 mutant (magenta) embryos. (D) Pairwise PCA scatterplots of morphogenetic parameters extracted from the datasets corresponding to the tracks in C. The major difference between control and neurog1hi1059 mutant embryos (PC1) corresponds to the antero-posterior axis.

Fig. 1.

Oriented cell movements are affected in neurog1hi1059 mutant embryos during olfactory cup formation. (A) Graphic representation of the morphogenesis of olfactory cup from 12 hpf to 27 hpf, showing a dorsal view of the three olfactory stages: olfactory territory (12 hpf), olfactory placode (18 hpf) and olfactory cup (24 hpf). EON progenitors are represented in green as visualised with the Tg(-8.4neurog1:gfp) transgene. At 12 hpf, the −8.4neurog1:GFP+ placodal domain can be divided into anterior, middle and posterior regions. The early (12-18 hpf; black) and late (18-27 hpf; grey) phases of morphogenesis are noted in the time line. (B) Tracks showing migration of EON of control (black) or neurog1hi1059 mutant (magenta) embryos. Twelve tracks are represented (two cells each from the left and right of three embryos) for each of the anterior, middle and posterior domains of the developing cup indicated in A. The origin of the tracks has been arbitrarily set to the intersection of the x/y-axes and the early (coloured) and late (grey) phases of migration have been highlighted. (C) Mean tracks for anterior EON of control (black) or neurog1hi1059 mutant (magenta) embryos. (D) Pairwise PCA scatterplots of morphogenetic parameters extracted from the datasets corresponding to the tracks in C. The major difference between control and neurog1hi1059 mutant embryos (PC1) corresponds to the antero-posterior axis.

To assess the morphogenetic phenotype of neurog1hi1059 mutant embryos at cellular resolution, we injected synthetic mRNAs encoding Histone2B-RFP (H2B-RFP) into Tg(-8.4neurog1:gfp) transgenic embryos, which were again imaged from 12 to 27 hpf. Morphogenetic parameters of individual EON located in the anterior, middle and posterior thirds of the initial neurog1:GFP+ population were extracted from datasets generated by manually tracking H2B-RFP-positive nuclei (Movies 2 and 3). The position of each tracked EON was then plotted relative to its origin. As for the global analysis, the behaviour we observe for single EON in control embryos largely recapitulates those already reported (Fig. 1B; Breau et al., 2017). Comparing the behaviour of EON in neurog1hi1059 mutants and siblings we found that, whereas EON in the middle and posterior regions of neurog1hi1059 mutant embryos migrate similarly to control siblings, the migratory behaviour of anterior EON is profoundly affected from 12 to 18 hpf (Fig. 1B,C; Fig. S2A); movements of individual skin cells showed no obvious differences in control versus neurog1hi1059 mutants, suggesting that the effect is specific to EON (Fig. S3A). Principal component analysis (PCA) of the datasets confirmed that the major difference between control and neurog1hi1059 mutant embryos (PC1) lies in the migratory behaviour of anterior EON along the AP axis (Fig. 1D); PCA revealed a more subtle difference in migration of the middle EON population along the same axis (Fig. S2B) and between the posterior EON populations along the superficial-deep axis (Fig. S2B). These migratory defects are not due to a decrease in cell mobility, as EON in neurog1 mutants displayed increased displacement over time compared with controls (Fig. S3B,C); little or no difference was detected in the displacement of skin cells between control and neurog1hi1059 mutant embryos (Fig. S3B,D). Taken together, our results indicate that Neurog1 is required between 12 and 18 hpf for the migratory behaviour of olfactory progenitors.

The chemokine receptor Cxcr4b and its ligand Cxcl12a have been implicated in olfactory cup morphogenesis in the zebrafish (Miyasaka et al., 2007). To address whether the behaviour of EON in neurog1hi1059 mutants resembles that caused when the activity of this guidance receptor/ligand pair is abrogated, we analysed the morphogenetic parameters of EON in cxcr4bt26035 and cxcl12at30516 mutants (Knaut et al., 2003; Valentin et al., 2007). As previously reported, olfactory progenitors in embryos lacking Cxcr4b or Cxcl12a function display convergence defects, highlighted by an increase in the AP length relative to controls (Fig. S4A; Movies 4 and 5; Miyasaka et al., 2007). Analysis of the behaviour of individual EON in cxcr4bt26035 and cxcl12at30516 mutant embryos indicates that defects in their migration are largely restricted to the anterior cohort (Fig. 2A,B; Fig. S5A,B); EON show increased displacement over time in both cxcr4bt26035 and cxcl12at30516 mutants (Fig. S4B,C) and no difference is apparent in the behaviour of skin cells in either mutant relative to control siblings (Figs S4B,D and S6). A combined PCA of datasets for anterior EON of neurog1hi1059, cxcr4bt26035 and cxcl12at30516 mutants confirms that the major difference in EON behaviour lies in their displacement along the AP axis (PC1; Fig. 2C). Finally, clustering of the PCA analysis reveals that there is more resemblance in the behaviour of anterior EON between the three mutants than between any single mutant and controls (Fig. 2D).

Fig. 2.

Morphogenetic defects in cxcr4bt26035 and cxcl12at30516 mutant embryos resemble those of neurog1hi1059. (A) Tracks showing migration of anterior EON from control (black), cxcr4bt26035 (blue) and cxcl12at30516 (green) embryos. Twelve anterior tracks are represented (two cells each from the left and right of three embryos). The origin of the tracks has been arbitrarily set to the intersection of the x/y-axes and the early (coloured) and late (grey) phases of migration have been highlighted. (B) Mean tracks showing migration of anterior EON of control (black), neurog1hi1059 (magenta), cxcr4bt26035 (blue) and cxcl12at30516 (green) mutant embryos. (C) Pairwise PCA scatterplots of morphogenetic parameters extracted from the datasets corresponding to the tracks in B. The major difference between control, neurog1hi1059, cxcr4bt26035 and cxcl12at30516 mutant embryos (PC1) corresponds to the antero-posterior axis. (D) Clustering analysis of morphogenetic parameters extracted from the datasets presented in B and analysed in C. One cluster, k1, contains almost exclusively control cells (black), whereas cells from neurog1hi1059 (magenta), cxcr4bt26035 (blue) and cxcl12at30516 (green) mutant embryos clustered together in k2, k3 and k4.

Fig. 2.

Morphogenetic defects in cxcr4bt26035 and cxcl12at30516 mutant embryos resemble those of neurog1hi1059. (A) Tracks showing migration of anterior EON from control (black), cxcr4bt26035 (blue) and cxcl12at30516 (green) embryos. Twelve anterior tracks are represented (two cells each from the left and right of three embryos). The origin of the tracks has been arbitrarily set to the intersection of the x/y-axes and the early (coloured) and late (grey) phases of migration have been highlighted. (B) Mean tracks showing migration of anterior EON of control (black), neurog1hi1059 (magenta), cxcr4bt26035 (blue) and cxcl12at30516 (green) mutant embryos. (C) Pairwise PCA scatterplots of morphogenetic parameters extracted from the datasets corresponding to the tracks in B. The major difference between control, neurog1hi1059, cxcr4bt26035 and cxcl12at30516 mutant embryos (PC1) corresponds to the antero-posterior axis. (D) Clustering analysis of morphogenetic parameters extracted from the datasets presented in B and analysed in C. One cluster, k1, contains almost exclusively control cells (black), whereas cells from neurog1hi1059 (magenta), cxcr4bt26035 (blue) and cxcl12at30516 (green) mutant embryos clustered together in k2, k3 and k4.

The similarity in the migration phenotype of EON in neurog1hi1059, cxcr4bt26035 and cxcl12at30516 mutant embryos suggests that the proneural transcription factor and the receptor/ligand couple act in the same pathway. Furthermore, the expression patterns of neurog1 and cxcr4b overlap extensively from early stages (Fig. S7); neurog1 and cxcl12a only overlap in the telencephalon at relative late stages (data not shown). To determine whether the expression of either the receptor or its ligand are affected in the absence of Neurog1, we assessed their expression in neurog1hi1059 mutant embryos. We found that cxcr4b expression is dramatically reduced or absent in EON progenitors at 12 and 15 hpf in this context (Fig. 3A); the expression of cxcr4b recovers in neurog1hi1059 mutant embryos from 18 hpf, a stage at which we have previously reported that the expression of a second bHLH proneural gene, neurod4, also becomes Neurog1-independent (Fig. 3A; Madelaine et al., 2011). Contrary to cxcr4b, the expression of cxcl12a is unaffected in neurog1hi1059 mutant embryos at all stages analysed (Fig. 3B). Taken together, these results suggest that the EON migration phenotype in neurog1hi1059 mutant embryos results from the lack of Cxcr4b during the early phase of olfactory cup morphogenesis.

Fig. 3.

Cxcr4b is the predominant downstream effector of Neurog1 during olfactory cup morphogenesis. (A) cxcr4b whole-mount in situ hybridisation at 12, 15 and 18 hpf in control and neurog1hi1059 mutant embryos. cxcr4b expression is dramatically reduced or absent in EON progenitors at 12 and 15 hpf in neurog1hi1059 mutant embryos (white dotted lines) but from 18 hpf the expression of cxcr4b recovers. (B) cxcl12a whole-mount in situ hybridisation at 12, 15 and 18 hpf in control and neurog1hi1059 mutant embryos, in which cxcl12a expression is not affected. (C) Tracks showing migration of anterior EON of control (black) embryos, neurog1hi1059 mutant embryos (magenta), neurog1hi1059 mutant embryos carrying the Tg(-8.4neurog1:cxcr4b) transgene (cyan) and control embryos carrying Tg(-8.4neurog1:cxcr4b) (light blue). Twelve anterior tracks are represented (from four embryos). The origin of the tracks has been arbitrarily set to the intersection of the x/y-axes and the early (coloured) and late (grey) phases of migration have been highlighted. (D) Mean tracks showing migration of anterior EON of the tracks in C. (E) Pairwise PCA scatterplots of morphogenetic parameters extracted from the datasets presented in D. The major difference between control, neurog1hi1059, and control or neurog1hi1059 with the rescue transgene (PC1) corresponds to the antero-posterior axis. (F) Clustering analysis of morphogenetic parameters extracted from the datasets presented in D and analysed in E. One cluster, k2, contains virtually exclusively neurog1hi1059 cells (magenta), whereas cells from control (black), rescue (cyan) and control/rescue (light blue) embryos clustered together in k1, k3 and k4. Scale bars: 100 µm.

Fig. 3.

Cxcr4b is the predominant downstream effector of Neurog1 during olfactory cup morphogenesis. (A) cxcr4b whole-mount in situ hybridisation at 12, 15 and 18 hpf in control and neurog1hi1059 mutant embryos. cxcr4b expression is dramatically reduced or absent in EON progenitors at 12 and 15 hpf in neurog1hi1059 mutant embryos (white dotted lines) but from 18 hpf the expression of cxcr4b recovers. (B) cxcl12a whole-mount in situ hybridisation at 12, 15 and 18 hpf in control and neurog1hi1059 mutant embryos, in which cxcl12a expression is not affected. (C) Tracks showing migration of anterior EON of control (black) embryos, neurog1hi1059 mutant embryos (magenta), neurog1hi1059 mutant embryos carrying the Tg(-8.4neurog1:cxcr4b) transgene (cyan) and control embryos carrying Tg(-8.4neurog1:cxcr4b) (light blue). Twelve anterior tracks are represented (from four embryos). The origin of the tracks has been arbitrarily set to the intersection of the x/y-axes and the early (coloured) and late (grey) phases of migration have been highlighted. (D) Mean tracks showing migration of anterior EON of the tracks in C. (E) Pairwise PCA scatterplots of morphogenetic parameters extracted from the datasets presented in D. The major difference between control, neurog1hi1059, and control or neurog1hi1059 with the rescue transgene (PC1) corresponds to the antero-posterior axis. (F) Clustering analysis of morphogenetic parameters extracted from the datasets presented in D and analysed in E. One cluster, k2, contains virtually exclusively neurog1hi1059 cells (magenta), whereas cells from control (black), rescue (cyan) and control/rescue (light blue) embryos clustered together in k1, k3 and k4. Scale bars: 100 µm.

If the absence of early cxcr4b expression in neurog1hi1059 mutants underlies the morphogenesis defects in this background, we hypothesised that restoring its expression should rescue these defects. To test this, we generated a transgenic line in which expression of the chemokine receptor is controlled by a −8.4 kb fragment of genomic DNA responsible for neurog1 expression in EON, Tg(-8.4neurog1:cxcr4b-mCherry), and introduced it into the neurog1hi1059 mutant background (Blader et al., 2003; Madelaine et al., 2011). Analysis of the migratory behaviour of anterior EON in neurog1hi1059 mutant embryos carrying the transgene indicates that they display oriented posterior migration similar to control embryos and siblings carrying the transgene (Fig. 3C,D; Movies 6 and 7). The similarity in the behaviour of the anterior EON is also evident after PCA analysis and clustering, where neurog1hi1059 mutant cells carrying the transgene group primarily with control cells with or without the transgene rather than mutant cells lacking the transgene (Fig. 3E,F). Restoring the expression of cxcr4b does not rescue the reduced EON cell numbers in neurog1hi1059 mutant embryos [neurog1−/−: 20.17±2.24 (mean±s.e.m.) versus neurog1−/−;Tg: 13.83±0.98], suggesting that the migration phenotype is caused by the lack of Cxcr4b guidance receptor and not the size of the EON population. Although we cannot exclude that there are other factors involved downstream of Neurog1, the similarity of the migration phenotype in neurog1 and cxcr4b mutant embryos suggests that Cxcr4b is the predominant downstream effector of Neurog1 during the early phase of olfactory cup morphogenesis.

Finally, we asked whether cxcr4b is a direct transcriptional target of Neurog1 by searching for potential Neurog1-dependent cis-regulatory modules (CRM) at the cxcr4b locus. Proneural transcription factors bind CANNTG sequences known as E-boxes, which are often found in clusters (Bertrand et al., 2002). We identified 18 E-box clusters in the sequences from −100 to +100 kb of the cxcr4b initiation codon, but only one of these clusters contains more than one of the CAA/GATG E-box sequence preferred by Neurog1 (Fig. 4A; data not shown; Madelaine and Blader, 2011). Coherent with a role for this E-box cluster in the regulation of cxcr4b expression, a transgenic line generated using a 35 kb fosmid clone that contains this cluster, TgFOS(cxcr4b:eGFP), shows robust expression of GFP in the olfactory cup (Fig. 4A,D). To investigate whether this cluster acts as a bona fide Neurog1-dependent CRM, we performed chromatin immunoprecipitation (ChIP) experiments. In the absence of a ChIP-compatible antibody against endogenous zebrafish Neurog1, we chose a strategy based on mis-expression of a Ty1-tagged form of Neurog1. Mis-expression of Neurog1-Ty1 efficiently induces the expression of deltaA, a known Neurog1 target, and cxcr4b, suggesting that tagging Neurog1 does not affect its transcriptional activity and that cxcr4b behaves as a Neurog1 target (Fig. 4B). We have previously shown that the deltaA locus contains two proneural regulated CRMs (Madelaine and Blader, 2011); whereas CRM HI is Neurog1-dependent, HII underlies regulation of deltaA by members of the Ascl1 family of bHLH proneural factors (Hans and Campos-Ortega, 2002; Madelaine and Blader, 2011). We found that ChIP against Neurog1-Ty1 after mis-expression effectively discriminates between the Neurog1-regulated HI and Ascl1-regulated HII CRM at the deltaA locus, thus providing a control for the specificity of our ChIP strategy (Fig. 4C). Similarly, we were able to ChIP the potential CRM containing the CAGATG E-box cluster at the cxcr4b locus, suggesting that this region is also a target for Neurog1 (Fig. 4C).

Fig. 4.

Neurog1 directly controls cxcr4b expression via an upstream cis-regulatory module (CRM). (A) Schematic of the cxcr4b locus, indicating the position of exons of the cxcr4b gene (orange) and E-box clusters, which are colour-coded depending on the nature of the E-box sequences. Also presented is the position of the genomic sequences found in the TgFOS(cxcr4b:eGFP) transgene. (B) qPCR analysis of the effect of Neurog1-Ty1mRNA mis-expression on the relative mRNA levels of the known Neurog1 target gene deltaA and cxcr4b. A significant increase in expression is detected for both genes. (C) ChIP using an antibody against Ty1 and chromatin prepared from 15 hpf embryos mis-expressing Neurog1-Ty1 mRNA (grey). Control (black) represents ChIP with IgG alone. (D) Single confocal sections of TgFOS(cxcr4b:eGFP) embryos at 24 hpf, showing eGFP expression in the olfactory cups, and either HuC/D expression or nuclear labelling (TOPRO). Embryos were injected with an sgRNA pair flanking the E-box-containing CRM at the cxcr4b locus plus or minus Cas9 as a control. Insets show HuC/D expression in both conditions. Data are mean±s.e.m. *P=0.01, ***P=0.0001 (two-tailed Student's t-test). n.s., not significant. Scale bars: 20 µm.

Fig. 4.

Neurog1 directly controls cxcr4b expression via an upstream cis-regulatory module (CRM). (A) Schematic of the cxcr4b locus, indicating the position of exons of the cxcr4b gene (orange) and E-box clusters, which are colour-coded depending on the nature of the E-box sequences. Also presented is the position of the genomic sequences found in the TgFOS(cxcr4b:eGFP) transgene. (B) qPCR analysis of the effect of Neurog1-Ty1mRNA mis-expression on the relative mRNA levels of the known Neurog1 target gene deltaA and cxcr4b. A significant increase in expression is detected for both genes. (C) ChIP using an antibody against Ty1 and chromatin prepared from 15 hpf embryos mis-expressing Neurog1-Ty1 mRNA (grey). Control (black) represents ChIP with IgG alone. (D) Single confocal sections of TgFOS(cxcr4b:eGFP) embryos at 24 hpf, showing eGFP expression in the olfactory cups, and either HuC/D expression or nuclear labelling (TOPRO). Embryos were injected with an sgRNA pair flanking the E-box-containing CRM at the cxcr4b locus plus or minus Cas9 as a control. Insets show HuC/D expression in both conditions. Data are mean±s.e.m. *P=0.01, ***P=0.0001 (two-tailed Student's t-test). n.s., not significant. Scale bars: 20 µm.

To address the importance of the E-box cluster in the regulation of cxcr4b expression, we employed a Crispr/Cas9 approach to delete this CRM using a pair of sgRNAs flanking the CRM (Fig. S8A). The sgRNA pair efficiently induces deletions in the targeted sequence, as judged by PCR on genomic DNA extracted from injected embryos (Fig. S8B). Injection of the sgRNA pair into TgFOS(cxcr4b:eGFP) transgenic embryos caused mosaic disruption of the eGFP expression pattern (Fig. 4D). Loss of TgFOS(cxcr4b:eGFP) transgene expression is not due to cell death, as eGFP-negative cells maintain the expression of the early neuronal marker HuC/D (insets in Fig. 4D). Taken together, the results from our ChIP and Crispr/Cas9 experiments strongly suggest that the CAGATG E-box cluster upstream of cxcr4b is regulated directly by Neurog1.

Neurog1 controls an early wave of neurogenesis in the zebrafish olfactory epithelium (Madelaine et al., 2011). As in invertebrates, control of neurogenesis by this proneural transcription factor is achieved via the transcriptional regulation of so-called neurogenic genes, such as deltaA and deltaD in the fish (Hans and Campos-Ortega, 2002; Madelaine and Blader, 2011). Our present study highlights that Neurog1 is also required for morphogenesis of the zebrafish peripheral olfactory sensory organ, in this case via its target gene cxcr4b. Thus, our data support a simple mechanism whereby Neurog1 couples neurogenesis with morphogenesis via the transcriptional regulation of distinct targets. It has previously been shown that members of the Neurog family regulate Delta1 (Dll1) and Cxcr4 expression in the mouse, and that development the olfactory epithelium in this model requires Neurog-family proneural factors (Beckers et al., 2000; Mattar et al., 2004; Shaker et al., 2012). Although it remains to be demonstrated, we propose that this parsimonious mechanism for coordinating the development of the olfactory system may have been conserved across vertebrates.

Fish husbandry and lines

All embryos were handled according to relevant national and international guidelines. French veterinary services and the ethics committee of the Féderation de Recherche en Biologie de Toulouse (C2EA no. 01) approved the protocols used in this study, with approval ID: A-31-555-01 and APAPHIS #3653-2016011512005922v6.

Fish were maintained at the Centre de Biologie du Développement, Centre de Biologie Intégrative zebrafish facility in accordance with the rules and protocols in place. The neurog1hi1059, cxcr4bt26035 and cxcl12at30516 mutant lines have previously been described (Golling et al., 2002; Knaut et al., 2003; Valentin et al., 2007), as has the Tg(-8.4neurog1:gfp)sb1 (Blader et al., 2003). Embryos were obtained through natural crosses and staged according to Kimmel et al. (1995).

Establishment of new transgenic lines

The Tg(-8.4neurog1:cxcr4b-mCherry) transgene was generated by first cloning the coding region of cxcr4b minus its endogenous stop codon in frame upstream of mCherry. The resulting cxcr4b-mCherry fusion coding sequence was transferred into the middle entry plasmid of the Tol2kit developed in the Chien lab (Kwan et al., 2007). The final transgene vector was generated using LR recombination with a previously described p5′-8.4neurog1 (Madelaine et al., 2011), the pME-cxcr4b-mCherry, and the p3E-polyA and pDestTol2pA/pDestTol2pA2 from the Tol2kit (Kwan et al., 2007). The line was then generated by co-injecting the transgene with mRNA encoding Tol2 transposase into freshly fertilised zebrafish embryos.

The TgFOS(cxcr4b:eGFP)fu10Tg transgenic line was generated using homologous recombination by replacing the second exon of cxcr4b by LynGFP in the Fosmid CH1073-406F3, followed by zebrafish transgenesis (Revenu et al., 2014). The first five amino acids encoded by the first exon of cxcr4b are fused to LynGFP, preventing targeting to the membrane. The GFP localises to the cytoplasm in this transgenic line.

In situ hybridisation, immunostaining and microscopy

In situ hybridisation was performed as previously described (Oxtoby and Jowett, 1993). Antisense DIG-labelled probes for cxcr4b and cxcl12a (David et al., 2002) were generated using standard procedures. In situ hybridisations were visualised using BCIP and NBT (Roche) as substrates.

Embryos were immunostained as previously described (Madelaine et al., 2011); the primary antibody used was mouse anti-HuC/D (1:500; 16A11, Molecular Probes), which was detected using Alexa Fluor 555 conjugated goat anti-mouse IgG diluted (1:1000; A-28180, Molecular Probes). Immunostained embryos were counterstained with Topro3 (T3605, Molecular Probes). Labelled embryos were imaged using an upright SP8 Leica confocal microscope and analysed using ImageJ and Imaris 8.3 (Bitplane) software.

Cell tracking in time-lapse confocal datasets

Embryos carrying the Tg(-8.4neurog1:gfp) transgene (Blader et al., 2003) were injected with synthetic mRNA encoding an H2B-RFP fusion protein; for analysis of the global behaviour of olfactory morphogenesis, un-injected embryos were used. Embryos were then grown to 12 hpf, at which point they were dechorionated and embedded for imaging in 0.7% low-melting point agarose in fish system water. A time-lapse series of confocal stacks (1 µm slice/180 µm deep) was generated of the anterior neural plate and flanking non-neural ectoderm on an upright Leica SP8 confocal microscope using a 25× HC Fluotar water-immersion objective. Confocal stacks were taken every 7 min until 27 hpf, when the olfactory rosette was clearly visible. The trajectory of anterior, middle and posterior EON cohorts was subsequently constructed using Imaris 8.3 analysis software (Bitplane). Briefly, H2B-RFP+; neurog1:GFP+ EON were followed manually in the x-, y- and z-axes, and the centre of the nucleus of the cell of interest was determined and ‘tagged’ in each frame. Tags were subsequently linked in Imaris to create the trajectories shown in Movies 1-7. The position of each tag was also extracted and used as the raw data for the track analysis described below. Unless mentioned, for each of three embryos, two anterior, middle and posterior cells from the left and right olfactory organs were tracked.

Track analysis

Track parameters were extracted from Imaris as CSV files and analysed using a custom script generated in R (The R Project for Statistical Computing, www.r-project.org). First, tracks were rendered symmetric across the left-right axis for ease of interpretation. Tracks were then colour coded according to their genotype and to the phase of migration (early, from 12-18 hpf; late, from 18-27 hpf) and plotted. Finally, the mean for each set of tracks was generated using the ‘RowMeans’ function and plots were generated. The R scripts and raw data files have been deposited on GitHub (https://github.com/BladerLab/Aguillon_2020).

PCA and clustering were performed using the built-in R function ‘prcomp’ from the ‘FactoMineR’ package and the ‘kmeans’ function from the ‘stats’ package, respectively. In the figures, PCA analysis is presented as a scatterplot of the data for the two parameters (PC1 and PC2) that vary the most amongst the parameters analysed. The variances listed for the principal components highlight the fraction of the specific variance relative to the sum of all variances (100%). For example, in Fig. 1D the first principal component (PC1) is the variance between the behaviour of control and neurog1−/− EON cells along the antero-posterior (x) axis, and it accounts for 68% of the total variance between all the parameters analysed. Finally, the ‘barplot’ function (‘graphics’ package) was used to represent either the EON or skin displacement behaviours.

ChIP and qPCR

ChIP experiments were performed as previously described using approximately 300 embryos (12-15 hpf) per immunoprecipitation (Wardle et al., 2006). Two to four separate ChIP experiments were carried out with corresponding independent batches of either control uninjected embryos or embryos injected with a synthetic mRNA encoding Neurog1-Ty1; ChIP-grade mouse anti-Ty1 (1:100; BB2, Sigma-Aldrich) was used. Primers used for qPCR on ChIPs were: cxcr4b CATATG cluster, fw 5′-CTACATCTAAAAATTGAAAGA-3′ and rev 5′-CAAACCCAACACCCCTACTG-3′; deltaA HI fw 5′-GCGGAATGAACCACCAACTT-3′ and rev 5′-GTGTGACTAAAGGTGTATGGGTG-3′; deltaA HII fw 5′-TATTGTGTGCAGGCGGAATA-3′ and rev 5′-GTTTGAATGGGCTCCTGAGA-3′.

Reactions were carried out in triplicates on a MyIQ device (Bio-Rad). The specific signals were calculated as the ratio between the signals with the Ty1 antibody and beads alone, and were expressed as percentage of chromatin input.

For qPCR experiments, to determine expression levels of cxcr4b and deltaA after mis-expression of Neurog1-Ty1, total RNAs were extracted from 20 injected embryos at 15 hpf using the RNeasy Mini Kit (Qiagen), and reverse-transcribed using the PrimeScript RT reagent kit (Ozyme) according to the supplier's instructions. q-PCR analyses were performed on a MyIQ device (Bio-Rad) with the SsoFast EvaGreen Supermix (Bio-Rad), according to the manufacturer's instructions. All experiments include a standard curve. Samples from embryos were normalised to the number of ef1a (eef1a1l1) mRNA copies. Primers for qPCR to determine the expression levels of cxcr4b and deltaA after mis-expression of Neurog1-Ty1 normalised to the expression of ef1a were: cxcr4b coding fw 5′-GCTGGCATATTTCCACTGCT-3′ and rev 5′-AGTGCACTGGACGACTCTGA-3′; deltaA coding fw 5′-CGGGTTTACAGGCATGAACT-3′ and rev 5′-ATTGTTCCTTTCGTGGCAAG-3′; ef1a fw 5′-GCATACATCAAGAAGATCGGC-3′ and rev 5′-GCAGCCTTCTGTGCAGACTTTG-3′.

Crispr/Cas9 deletion of potential CRM at the cxcr4b locus

sgRNA sequences flanking the CAGATG E-box cluster at the cxcr4b locus were designed using the web-based CRIPSRscan algorithm (Moreno-Mateos et al., 2015; http://www.crisprscan.org). The targeted sequences are 5′-GGCTTATGATGGAGGCGACTGG-3′ and 5′-GGCTTGTATTGCCCTTGAGGG-3′; the PAM sequences at the target site are underlined. Templates for the transcription of sgRNAs were generated by PCR following previously described protocols (Nakayama et al., 2014). Injection of sgRNAs was performed as described by Burger et al. (2016), using a commercially available Cas9 protein (New England Biolabs). The efficiency of creating deletion after co-injection of the sgRNA pair was determined by PCR on genomic DNA extracted from injected embryos using the following primers: 5′-AACTCGCATTCGGCAAACTCTC-3′ and 5′-AAGGGGATAATGAGCAGTCAGC-3′. Although a 500 base-pair PCR fragment is generated from a wild-type locus, an ∼200 base-pair fragment is amplified if a deletion has been induced.

We thank Kristen Kwan and Chi-Bin Chien for providing plasmids of the Tol2kit, Stéphanie Bosch, Brice Ronsin and the Toulouse LITC RIO Imaging platform, and Aurore Laire and Richard Brimicombe for taking care of the fish. We also thank Marie Breau, Magali Suzanne, Christian Mosimann and members of the Blader lab for advice on experiments and comments on the manuscript.

Author contributions

Conceptualization: R.A., R.M., H.G., V.L., G.B., P.B., J.B.; Software: M.A., J.B.; Validation: J.B.; Formal analysis: R.A., R.M., H.G., S.L., P.D., V.L., G.B., J.B.; Investigation: R.A., R.M., H.G., S.L., P.D., V.L., G.B., J.B.; Data curation: R.A., M.A., P.B., J.B.; Writing - original draft: R.A., P.B., J.B.; Supervision: P.D., V.L., G.B., P.B., J.B.; Project administration: P.B., J.B.; Funding acquisition: P.B.

Funding

This work was supported by the Centre National de la Recherche Scientifique (CNRS); the Institut National de la Santé et de la Recherche Médicale (INSERM); Université de Toulouse III (UPS); Fondation pour la Recherche Médicale (FRM; DEQ20131029166); Fédération pour la Recherche sur le Cerveau (FRC); and the Ministère de l'Enseignement Supérieur et de la Recherche.

Data availability

R scripts and raw data files from track analysis are available at GitHub (https://github.com/BladerLab/Aguillon_2020).

Supplementary information

Supplementary information available online at https://dev.biologists.org/lookup/doi/10.1242/dev.192971.supplemental

Beckers
,
J.
,
Caron
,
A.
,
Hrabé de Angelis
,
M.
,
Hans
,
S.
,
Campos-Ortega
,
J. A.
and
Gossler
,
A.
(
2000
).
Distinct regulatory elements direct delta1 expression in the nervous system and paraxial mesoderm of transgenic mice
.
Mech. Dev.
95
,
23
-
34
.
Bertrand
,
N.
,
Castro
,
D. S.
and
Guillemot
,
F.
(
2002
).
Proneural genes and the specification of neural cell types
.
Nat. Rev. Neurosci.
3
,
517
-
530
.
Blader
,
P.
,
Plessy
,
C.
and
Strähle
,
U.
(
2003
).
Multiple regulatory elements with spatially and temporally distinct activities control neurogenin1 expression in primary neurons of the zebrafish embryo
.
Mech. Dev.
120
,
211
-
218
.
Breau
,
M. A.
,
Bonnet
,
I.
,
Stoufflet
,
J.
,
Xie
,
J.
,
De Castro
,
S.
and
Schneider-Maunoury
,
S.
(
2017
).
Extrinsic mechanical forces mediate retrograde axon extension in a developing neuronal circuit
.
Nat. Commun.
8
,
282
.
Burger
,
A.
,
Lindsay
,
H.
,
Felker
,
A.
,
Hess
,
C.
,
Anders
,
C.
,
Chiavacci
,
E.
,
Zaugg
,
J.
,
Weber
,
L. M.
,
Catena
,
R.
,
Jinek
,
M.
,
Robinson
,
M. D.
and
Mosimann
,
C.
(
2016
)
Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes
.
Development
143
,
2025
-
2037
.
David
,
N. B.
,
Sapede
,
D.
,
Saint-Etienne
,
L.
,
Thisse
,
C.
,
Thisse
,
B.
,
Dambly-Chaudiere
,
C.
,
Rosa
,
F. M.
and
Ghysen
,
A.
(
2002
).
Molecular basis of cell migration in the fish lateral line: role of the chemokine receptor CXCR4 and of its ligand, SDF1
.
Proc. Natl. Acad. Sci. USA
99
,
16297
-
16302
.
Golling
,
G.
,
Amsterdam
,
A.
,
Sun
,
Z.
,
Antonelli
,
M.
,
Maldonado
,
E.
,
Chen
,
W.
,
Burgess
,
S.
,
Haldi
,
M.
,
Artzt
,
K.
,
Farrington
,
S.
, et al. 
(
2002
).
Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development
.
Nat. Genet.
31
,
135
-
140
.
Hans
,
S.
and
Campos-Ortega
,
J. A.
(
2002
).
On the organisation of the regulatory region of the zebrafish deltaD gene
.
Development
129
,
4773
-
4784
.
Kimmel
,
C. B.
,
Ballard
,
W. W.
,
Kimmel
,
S. R.
,
Ullmann
,
B.
and
Schilling
,
T. F.
(
1995
).
Stages of embryonic development of the zebrafish
.
Dev. Dyn.
203
,
253
-
310
.
Knaut
,
H.
,
Werz
,
C.
,
Geisler
,
R.
,
Nüsslein-Volhard
,
C.
and
Tubingen Screen
,
C.
(
2003
).
A zebrafish homologue of the chemokine receptor Cxcr4 is a germ-cell guidance receptor
.
Nature
421
,
279
-
282
.
Kwan
,
K. M.
,
Fujimoto
,
E.
,
Grabher
,
C.
,
Mangum
,
B. D.
,
Hardy
,
M. E.
,
Campbell
,
D. S.
,
Parant
,
J. M.
,
Yost
,
H. J.
,
Kanki
,
J. P.
and
Chien
,
C.-B.
(
2007
).
The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs
.
Dev. Dyn.
236
,
3088
-
3099
.
Madelaine
,
R.
and
Blader
,
P.
(
2011
).
A cluster of non-redundant Ngn1 binding sites is required for regulation of deltaA expression in zebrafish
.
Dev. Biol.
350
,
198
-
207
.
Madelaine
,
R.
,
Garric
,
L.
and
Blader
,
P.
(
2011
).
Partially redundant proneural function reveals the importance of timing during zebrafish olfactory neurogenesis
.
Development
138
,
4753
-
4762
.
Mattar
,
P.
,
Britz
,
O.
,
Johannes
,
C.
,
Nieto
,
M.
,
Ma
,
L.
,
Rebeyka
,
A.
,
Klenin
,
N.
,
Polleux
,
F.
,
Guillemot
,
F.
and
Schuurmans
,
C.
(
2004
).
A screen for downstream effectors of Neurogenin2 in the embryonic neocortex
.
Dev. Biol.
273
,
373
-
389
.
Miyasaka
,
N.
,
Knaut
,
H.
and
Yoshihara
,
Y.
(
2007
).
Cxcl12/Cxcr4 chemokine signaling is required for placode assembly and sensory axon pathfinding in the zebrafish olfactory system
.
Development
134
,
2459
-
2468
.
Miyasaka
,
N.
,
Wanner
,
A. A.
,
Li
,
J.
,
Mack-Bucher
,
J.
,
Genoud
,
C.
,
Yoshihara
,
Y.
and
Friedrich
,
R. W.
(
2013
).
Functional development of the olfactory system in zebrafish
.
Mech. Dev.
130
,
336
-
346
.
Moreno-Mateos
,
M. A.
,
Vejnar
,
C. E.
,
Beaudoin
,
J.-D.
,
Fernandez
,
J. P.
,
Mis
,
E. K.
,
Khokha
,
M. K.
and
Giraldez
,
A. J.
(
2015
).
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
.
Nat. Methods
12
,
982
-
988
.
Nakayama
,
T.
,
Blitz
,
I. L.
,
Fish
,
M. B.
,
Odeleye
,
A. O.
,
Manohar
,
S.
,
Cho
,
K. W. Y.
and
Grainger
,
R. M.
(
2014
).
Cas9-based genome editing in Xenopus tropicalis
.
Methods Enzymol.
546
,
355
-
375
.
Oxtoby
,
E.
and
Jowett
,
T.
(
1993
).
Cloning of the zebrafish krox-20 gene (krx-20) and its expression during hindbrain development
.
Nucleic Acids Res.
21
,
1087
-
1095
.
Revenu
,
C.
,
Streichan
,
S.
,
Dona
,
E.
,
Lecaudey
,
V.
,
Hufnagel
,
L.
and
Gilmour
,
D.
(
2014
).
Quantitative cell polarity imaging defines leader-to-follower transitions during collective migration and the key role of microtubule-dependent adherens junction formation
.
Development
141
,
1282
-
1291
.
Shaker
,
T.
,
Dennis
,
D.
,
Kurrasch
,
D. M.
and
Schuurmans
,
C.
(
2012
).
Neurog1 and Neurog2 coordinately regulate development of the olfactory system
.
Neural Dev.
7
,
28
.
Valentin
,
G.
,
Haas
,
P.
and
Gilmour
,
D.
(
2007
).
The chemokine SDF1a coordinates tissue migration through the spatially restricted activation of Cxcr7 and Cxcr4b
.
Curr. Biol.
17
,
1026
-
1031
.
Wardle
,
F. C.
,
Odom
,
D. T.
,
Bell
,
G. W.
,
Yuan
,
B.
,
Danford
,
T. W.
,
Wiellette
,
E. L.
,
Herbolsheimer
,
E.
,
Sive
,
H. L.
,
Young
,
R. A.
and
Smith
,
J. C.
(
2006
).
Zebrafish promoter microarrays identify actively transcribed embryonic genes
.
Genome Biol.
7
,
R71
.
Whitlock
,
K. E.
and
Westerfield
,
M.
(
1998
).
A transient population of neurons pioneers the olfactory pathway in the zebrafish
.
J. Neurosci.
18
,
8919
-
8927
.
Whitlock
,
K. E.
and
Westerfield
,
M.
(
2000
).
The olfactory placodes of the zebrafish form by convergence of cellular fields at the edge of the neural plate
.
Development
127
,
3645
-
3653
.

Competing interests

The authors declare no competing or financial interests.