Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr
© Ahi et al. 2015
Received: 15 July 2015
Accepted: 4 September 2015
Published: 16 September 2015
The developmental basis of craniofacial morphology hinges on interactions of numerous signalling systems. Extensive craniofacial variation in the polymorphic Arctic charr, a member of the salmonid family, from Lake Thingvallavatn (Iceland), offers opportunities to find and study such signalling pathways and their key regulators, thereby shedding light on the developmental pathways, and the genetics of trophic divergence.
To identify genes involved in the craniofacial differences between benthic and limnetic Arctic charr, we used transcriptome data from different morphs, spanning early development, together with data on craniofacial expression patterns and skeletogenesis in model vertebrate species. Out of 20 genes identified, 7 showed lower gene expression in benthic than in limnetic charr morphs. We had previously identified a conserved gene network involved in extracellular matrix (ECM) organization and skeletogenesis, showing higher expression in developing craniofacial elements of benthic than in limnetic Arctic charr morphs. The present study adds a second set of genes constituting an expanded gene network with strong, benthic–limnetic differential expression. To identify putative upstream regulators, we performed knowledge-based motif enrichment analyses on the regulatory sequences of the identified genes which yielded potential binding sites for a set of known transcription factors (TFs). Of the 8 TFs that we examined using qPCR, two (Ahr2b and Ap2) were found to be differentially expressed between benthic and limnetic charr. Expression analysis of several known AhR targets indicated higher activity of the AhR pathway during craniofacial development in benthic charr morphotypes.
These results suggest a key role of the aryl hydrocarbon receptor (AhR) pathway in the observed craniofacial differences between distinct charr morphotypes.
In cichlids, transcriptional changes of major signalling pathways during early craniofacial development have been attributed to phenotypic novelties in trophic architecture [20, 21]. Associations between heterochronic shifts in the expression levels of individual skeletogenic genes and distinct craniofacial morphogenesis were indicated in several fish species [22–24]. However, it is not always the case that expression differences of a specific gene result in changes in its protein levels and subsequent phenotypic effects . Instead, looking for transcriptional differences in sets of functionally related genes with conserved co-expression connectivity might provide more reliable evidence concerning the involvement of genes in a specific biological process . More recently, similar efforts have been made to define co-expression gene networks involved in adaptive phenotypic divergence of feeding structures in an East African cichlid species  and two salmonid species (Arctic charr and whitefish) [19, 28]. We previously identified a conserved co-expression network consisting of genes involved in extracellular matrix (ECM) organization and skeletogenesis, which was more expressed in the developing craniofacial elements of benthic than in limnetic Arctic charr morphs . Many of these genes are known as downstream targets of several inter-connected regulatory pathways . It is possible that the molecular mechanisms underlying induction of this gene network also affect (activate/repress) other genes and possibly co-expressed networks of genes involved in craniofacial development and skeletogenesis. The identification of groups of genes with tight positive or negative co-expression could provide clues about upstream molecular pathways [29, 30] and even causative genetic changes.
In this study, we investigated transcriptional profiles in developing heads of benthic and limnetic Arctic charr morphs focusing on the period when key elements of the feeding structures are being formed, and, notably, a period when the basis of the benthic–limnetic distinction may be laid . Using transcriptome data of contrasting Arctic charr morphs and through a stepwise approach assisted by co-expression data from mammalian species, we identified genes with higher expression during the morphogenesis of limnetic charr heads. Furthermore, to identify potential upstream regulators, we performed knowledge-based motif enrichment analyses on the regulatory sequences of a network of co-expressed genes (including the identified genes) to predict binding sites for known transcription factors (TFs). Finally, we found Ahr2b and other components of a signalling pathway mediated by aryl hydrocarbon receptor (AhR) to be differentially expressed between benthic and limnetic charr, which is consistent with the AhR pathway being a regulator of morph-specific, transcriptional dynamics. These results provide a glimpse into the regulatory networks that seem to shape craniofacial traits in Arctic charr and possibly other teleosts.
Fish stocks and sampling
We sampled sexually ripe adults of the four sympatric morphs from Lake Thingvallavatn; planktivorous (small limnetic) (PL), piscivorous (PI), small benthivorous (SB) and large benthivorous (LB) morphs, and a limnetic-like aquaculture stock (AC) from the Hólar breeding programme . For each morph, eggs from several females were pooled and fertilized using milt from several males. Eggs were reared at approximately 5 °C in hatching trays (EWOS, Norway) under constant water flow and in complete darkness at Holar College experimental facilities in Verið, Sauðárkrókur. The water temperature was recorded twice daily and the average was used to estimate the relative age of the embryos using tau-somite (τ s) units, defined as the time it takes for one somite pair to form at a given temperature . All sampling from the wild as well as rearing was performed according to Icelandic law and with appropriate permission.
Genes, databases and overrepresentation analysis
Based on an extensive literature survey and analyses of transcriptome data from early embryonic stages of contrasting Arctic charr morphs (unpublished), we selected our initial sets of candidate genes (see “Results” section) that play a role in craniofacial morphogenesis and/or skeletogenesis, for gene expression profiling. We also checked whether the orthologues of the candidate genes show co-expression relationship in data from mammalian species using COXPRESdb (http://coxpresdb.jp/) version 6.0 ). To predict the potential regulators of the genes with reduced expression levels during benthic head development, TF enrichment analysis was conducted using the list of >200 genes co-expressed with Chd4, Cspp1 and Dlg1 in humans and mice, as well as the WEB-based GEne SeT AnaLysis Toolkit (WebGestalt) v2 . The involvement of the AhR was investigated by profiling the expression of 12 genes responsive to the pathway which also have been shown to be expressed during craniofacial development in fish and/or involved in vertebrate skeletal formation (Additional file 1: Table S1).
RNA isolation, cDNA synthesis and primer design for qPCR
We studied embryos of five Arctic charr morphs, collected at 6 tau-somite stages (178, 200, 216, 238, 256 and 275 τ s). This is the period during which the morphs start developing their distinct craniofacial morphologies . The time points span early craniofacial cartilage formation, 178 (τ s), to a pre-hatching stage, when ossification of key trophic elements of the jaws has started at 275 (τ s). The embryos were preserved in RNA-later solution (Ambion) at −20 °C and later dechorionated and decapitated by applying a scalpel vertically in front of the pectoral fin under the light microscope (Leica S6E). For each morph and time-point, two RNA extraction replicates were obtained, each one deriving from six heads. Extractions were conducted in TRI Reagent (Sigma). The heads were homogenized with a disposable Kontes Pellet Pestle Cordless Motor tissue grinder (Kimble Kontes). RNA was extracted according to the manufacturer’s instructions, and DNA contamination was removed by DNase treatment (New England Biolabs). The quantification and quality control of RNA were performed using a NanoDrop ND-1000 UV/Vis-Spectrophotometer (NanoDrop Technologies) and agarose gel electrophoresis. cDNA was synthesized with 1 µg of RNA in a total reaction volume of 20 µl using the High Capacity cDNA RT kit (Applied Biosystems). cDNA was diluted threefold in nuclease-free water for further use in qPCR and several samples without addition of reverse transcriptase were prepared to confirm the absence of genomic DNA. An assembly of the Arctic charr transcriptome  was used for qPCR primer design. It is important to note that a whole genome duplication event occurred before the radiation of the salmonid family producing paralogues, most of which are retained in Arctic charr . In this study, we were not focusing on differences between paralogues in expression or function and therefore designed primers to be non-paralogue specific. The only exception is Ahr2b where we looked at differential expression of two paralogues as discussed below. To identify the conserved exon/intron boundaries of the candidate genes, the assembled charr contigs were aligned to the genomic sequences of salmon orthologs (retrieved from the salmon database, SalmonDB ) using the NCBI Spidey software (http://www.ncbi.nlm.nih.gov/spidey). Primers were designed using Primer Express 3.0 software (Applied Biosystems, Foster City, CA, USA) and checked for self-annealing, hetero-dimers and hairpin structures by OligoAnalyzer 3.1 (Integrated DNA Technology) (Additional file 2: Table S2).
Real-time quantitative PCR and analysis of expression data
Real-time PCR was performed in 96-well PCR plates on an ABI 7500 real-time PCR System (Applied Biosystems) using Fermentas Maxima SYBR Green qPCR Master Mix (2x) (Fermentas). Each biological replicate was run in duplicate together with no-template control (NTC) in each run for each gene. The PCR was run with a 2 min hold at 50 °C and a 10 min hot start at 95 °C followed by the amplification step for 40 cycles of 15 s denaturation at 95 °C and 1 min annealing/extension at 60 °C. A dissociation step (60–95 °C) was performed at the end of the amplification phase to identify a single, specific melting temperature for each primer set. Primer efficiency values (E) were calculated through the LinRegPCR v11.0 programme (http://LinRegPCR.nl)  analysing the fluorescence data from the exponential phase of PCR amplification for each primer pair (Additional file 2: Table S2) and the cut-off was 0.9. The difference between Cq values (ΔCq) of the reference genes and the target genes was calculated for each gene t; ΔCqtarget = Cqtarget − Cqreference. The geometric mean of Cq values of two validated craniofacial reference genes, Actb and If5a1, was used for ΔCq calculations . All samples were then normalized to the ΔCq value of a calibrator sample to obtain a ΔΔCq value (ΔCqtarget − ΔCqcalibrator). For visual comparisons of expression levels among the developmental time-points and morphs, the biological replicate with the lowest expression (highest ΔCq) was used as a calibrator sample. Relative expression quantities (RQ) were calculated based on the expression level of the calibrator sample (E −ΔΔCq) . The RQ values were then transformed to logarithmic base 2 values (or fold differences; FD)  for statistical analysis. A two-way ANOVA followed by Tukey’s HSD post hoc tests were implemented to examine the effects of morph, time, and morph-by-time interaction on expression of the candidate genes as well as morph-specific expression difference for each gene. To assess similarity in expression patterns of the genes, Pearson correlation coefficients (r) were calculated for all gene pairs using the data from 5 morphs at 6 time-points (df = 28). To study the relationships between putative regulators and candidate genes, we calculated the correlation (Pearson and Kendall) between all candidate genes (including AhR targets) and the 9 potential regulators (8 predicted TFs and Foxq1, an AhR-regulated TF). Next, we tested whether the correlation coefficients varied between TFs or gene categories (higher, lower or equally expressed in benthic morphs), using ANOVAs and non-parametric. R (http://www.r-project.org) was used for all statistical analysis .
Whole-mount in situ hybridization (WISH)
Whole-mount in situ hybridization was performed following a standard procedure for Atlantic salmon . Embryos from a time-point (238 τ s) representing the early craniofacial bone and cartilage formation were fixed in 4 % (m/v) paraformaldehyde/PBS, dehydrated in a graded methanol series and stored in 100 % methanol. Primers designed for cDNA of selected Arctic charr genes (Ahr2b, Apaf1, Cfl1, Foxq1, Jup, Chd4, Cspp1, and Dlg1) generated PCR products of around 0.4–0.6 kbp (Additional file 2: Table S2) which were cloned into pCR4-TOPO vector (Invitrogen) and transcribed to antisense/sense digoxigenin (DIG)-labelled cRNA probes with T3 or T7 polymerases (Roche). Five or six embryos from each of the two morphs (PL and SB) were used for in situ hybridization at every relative age. After rehydration and dechlorination, embryos were treated with 20–40 µg/ml proteinase K (New England Biolabs) for 22–60 min, depending on the relative ages. The hybridization was performed with 1 µg/ml (DIG)-labelled RNA probes at 70 °C for 12 h, after which the embryos were incubated with alkaline phosphatase-conjugated anti-digoxigenin antibody (Roche) at 4 °C overnight. The hybridization signals were visualized after 3–12 h incubation at 4 °C using NBT/BCIP (Roche), depending on the expression levels of the genes. The specificity of the antisense probes was also verified by running control experiments with sense probes. Samples were imaged on a Leica MZ10 binocular microscope (Leica).
A group of transcriptionally correlated genes shows higher expression in the head of limnetic than benthic morphs
Potential upstream regulators of the co-expressed genes
Differentially expressed AhR target genes show transcriptional correlation with the previously identified genes
To further assess expression associations between the TFs and the other genes studied here, we calculated the correlation between expression levels of all the genes together and the TFs (Fig. 6b, Additional file 5: Figure S1). The genes were classified into three categories, “Up”, “Down” and “Rest” based on significant expression differences between benthic and limnetic morphotypes. Genes in the Up group had higher expression in benthic charr, while the Down group showed lower expression in benthic charr. The Rest category consists of genes with no significant expression differences between the two morphotypes. As was predicted, Ahr2b showed significant positive correlation with its target genes (Up-genes in Fig. 6b) and a negative, but weak relationship with the Down-genes group. Ahr2b levels did not associate on average with genes in the Rest group. The Down genes were positively correlated with six of the other candidate regulators (Ap2, E2f1, Maz, Nrf1, Sp1 and Yy1) (Fig. 6b, Additional file 5: Figure S1), of which only Ap2 differed significantly between the morphotypes. The opposite effect, i.e. negative correlation with the Up genes, was generally not observed for these other TFs. Curiously, however, these factors all showed positive correlation with genes of the Rest category. The correlation of Foxq1 expression with the three groups of genes was similar to that seen for Ahr2b, except Foxq1, which is a TF known to be activated by AhR signalling, showed stronger negative association with the Down genes (Fig. 6b).
To summarize the overall patterns of expression, we conducted double hierarchical clustering of relative expression values of genes vs. morph and time (Fig. 6c). The genes are divided into two main branches. The AhR targets and Ahr2b (in bold) clustered in one branch and the rest of the genes with reduced expression in benthic morphs (including Ap2 and Apaf1) clustered in the other branch. Predictably, the clustering of samples (morph-time) revealed a separation of morphotypes with benthic morphs (red bar) on one of the two main branches and the limnetic morphs (black bar) on the other. The exceptions to this were PL and PI at early time-points, and AC which clustered with the benthic samples at the last time-point (Fig. 6c). Taken together, these results suggest higher activity in the AhR signalling pathway, probably through Ahr2b, during the craniofacial development of benthic Arctic charr morphs.
Craniofacial expression patterns of differentially expressed genes
An increasing number of gene expression studies have been launched to unravel the molecular mechanisms underlying adaptive morphological novelties in feeding structures of a variety of fish species [19–23, 27, 28, 66, 67]. Developmental shifts in the relative timing of skeletal gene expression, i.e. collagen genes, have been shown to underpin the radiation of feeding structures in Antarctic notothenioid fish along the benthic–limnetic axis of habitat . Similarly, a heterochronic shift in developmental expression of a Calmodulin gene has been suggested to drive the variable growth rates of the jaws across Belonoid fishes . In addition to the heterochrony in expression, the developmental differences in the level of gene expression have been repeatedly linked to occurrence of adaptive skeletal changes in teleost fish [19–21, 28, 68, 69]. It is important to note that a highly similar skeletal phenotype might emerge from the altered expression of different regulatory genes as two distinct transcriptional mechanisms give rise to the loss of pelvic skeleton in stickleback and fugu [69, 70]. Studies in cichlids have shown that genetic changes in regulatory elements may account for altered expression of genes involved in skeletogenesis and the subsequent morphological variations [20, 71, 72]. Also, external stimulants during early development, such as mechanical strain in bone, can alter the expression of skeletal genes (e.g. ECM genes) and result in adaptive phenotypic plasticity in feeding structures [27, 66]. The molecular basis of adaptive morphological novelties in feeding structures can be further elucidated through the expression analysis of functionally and transcriptionally related gene networks. The identification of such gene network provides a promising foundation to investigate potential upstream regulatory elements and interacting signalling pathways [26, 29, 30]. The related examples include the identification of gene expression networks associated with evolution of oral jaw dentition  and pharyngeal jaw developmental plasticity  in East African cichlids, as well as craniofacial skeletal diversity in sympatric Arctic charr  and lake whitefish .
Recently, we identified a gene network involved in ECM organization, cell-substrate adhesion and skeletogenesis with higher levels of expression in developing heads of benthivorous Arctic charr than in limnetic morphs . In the same study, we predicted several transcription factors, such as Ap1 and Ets2, as potential regulators of the network. Although these TFs could be key elements causing the induction of the ECM-related gene network, they are likely to be regulated through pathways further upstream. Such upstream pathways might also regulate other gene networks involved in craniofacial morphogenesis. In general, the activation of a particular signalling pathway leads to both induction and repression of different sets of downstream genes during embryonic development . Therefore, we set out to search for co-expressed genes involved in skeletogenesis/craniofacial formation focusing on genes that had higher expression during head development in limnetic than in benthic morphs of Arctic charr. Such genes may be a part of networks that are transcriptionally linked to the previously described ECM-related gene network through common upstream regulatory elements.
In an iterative selection for co-expressed genes, we found seven candidate genes, Chd4, Cspp1, Dlg1, Hcfc1, Kdm5c, Rev3 l and Whsc1, showing reduced expression in benthic morphs. In a recent study on mammalian embryonic cells, Chd4 has been shown to be a potent co-repressor of sry-box containing gene 9 (Sox9), a highly conserved gene involved in skeletal development . While the role of Chd4 in craniofacial development has not been investigated, other genes such as Cspp1, Dlg1, Hcfc1 and Whsc1 are well known to be essential for normal development of craniofacial skeletal elements [55–57, 59]. In our study, the positive expression correlation of these genes could suggest their co-regulation through shared transcriptional regulatory elements during Arctic charr head development. Using co-expression data from mammals , we found over 200 genes to be co-expressed with Chd4, Cspp1 and Dlg1 as well as with at least one of the other identified genes. Binding sites for 17 TFs were significantly enriched on the promoter regions of these genes in human and mouse. By profiling the expression of eight predicted TFs with most significantly overrepresented binding sites, we found two of them, Ahr2b and Ap2, to be differentially expressed between benthic and limnetic morphotypes. Curiously, a zebrafish Ahr2 mutant displays an extension of the ethmoid and mandibular regions, shallower head and longer snout which is a reminiscent phenotype of limnetic Arctic charr morphology [16, 65]. Furthermore, Ap2-dependent signals from epithelium have been demonstrated to induce skeletogenesis during craniofacial development in zebrafish . It is unclear, however, whether Ahr2 and Ap2 show a direct transcriptional interaction during development.
Aryl hydrocarbon receptor (Ahr) belongs to the basic-helix-loop-helix (bHLH)/Per-Arnt-Sim (PAS) family of heterodimeric transcriptional regulators and it was originally described as a receptor that mediates many of the toxic effects of environmental contaminants of the dioxin family . It is highly unlikely that the actual role of AhR is to sense environmental contaminants, but the search for endogenous ligands is still ongoing (reviewed in ). There is, however, increasing evidence that the AhR pathway plays important roles in a variety of developmental, physiological and immunological processes [75, 77–81]. The pathological effects of AhR pathway induction in zebrafish are exerted mostly through the transcriptional regulation of a large number of downstream genes . It is also known that the activation of the AhR pathway not only alters the expression of ECM remodelling genes, but the pathway itself can also be affected by changes in ECM organization and cell-substrate adhesion . Many of the identified TF binding sites in this study (such as binding sites for Ahr, Ap2, E2f1, Max, Myc, Myb, Nf1, Sp1, Usf, and Yy1) (Additional file 4: Table S4) are also predicted on the promoter of AhR-regulated genes in mammals [78, 84]. This suggests that these TFs cooperate in the regulation of AhR target genes that could be conserved across vertebrates. To further investigate the involvement of the AhR pathway, we examined the transcriptional dynamics of 12 downstream targets of the pathway which were selected based on existing literature of their craniofacial expression pattern and/or their role in vertebrate skeletal formation (Additional file 1: Table S1). All of these candidates, except Apaf1, are known to be induced by activation of the AhR pathway. Accordingly, we found higher expression of most candidates in developing heads of benthic morphs, whereas only Apaf1 displayed reduced expression relative to limnetic morphs (known to be down regulated by AhR). Most of the AhR-regulated candidates as well as Ahr2b had negative expression correlation with the seven genes identified at the beginning of this study and only Apaf1 showed positive expression correlations with them (Fig. 6a). The AhR-regulated candidates also had positive expression correlation with the previously identified co-expression network of ECM genes during the same developmental time-points (, data not shown). These results suggest higher activity of the AhR pathway during head development of benthic than limnetic morphs.
In Atlantic salmon, multiple aryl hydrocarbon receptor genes are reported, four of which are paralogues of Ahr2, with markedly higher expression than the two paralogues of Ahr1 . Here, we only report results for one Ahr2 paralogue (Ahr2b) which had the highest expression level in a developmental transcriptome of Arctic charr . Two other paralogues (Ahr2a and Ahr2c) were not detected in the transcriptome data, whereas the third one (Ahr2d) was identified with lower expression but qPCR analysis with paralogue specific primers showed no differences in expression between benthic and limnetic morphs (data not shown). Developmental effects of AhR pathway activation on skeletogenesis are mediated by Ahr2 in zebrafish and transcriptional suppression of Ahr2 could partially rescue the resulting inhibition of jaw chondrogenesis during development . Analysis of the non-functional Ahr2 mutant in zebrafish illustrated the endogenous role of the AhR pathway in craniofacial development , but the molecular mechanism for this craniofacial effect has remained unclear. So far, investigation of potential downstream targets in zebrafish identified a contribution of Sox9 to AhR-induced jaw malformation . In a previous study, we did not detect such differential expression of Sox9 at early stages of craniofacial skeletal formation in different Arctic charr morphs . In zebrafish, down-regulation of the Sox9 isoform (Sox9b) does not occur immediately after induction of AhR pathway which might suggest an indirect mechanism for AhR regulation of Sox9b . It has been reported that Ap2 negatively regulates chondrocyte differentiation by suppressing Sox5/6, but not Sox9 . In contrast to Ahr2b, the higher expression of Ap2 in limnetic morphs and the reduced jaw skeleton and shorter snout of Ap2 mutant in zebrafish [65, 74] suggest counteracting roles for Ap2 and Ahr2b in mediating differential effects on craniofacial skeletogenesis.
Cyp1a1 is known as the most potently induced AhR target , and its expression has been identified in craniofacial tissues of teleost fish species . In our study, Cyp1a1 shows strong benthic–limnetic expression differences (Fig. 5). A functional study revealed that suppression of Cyp1a1 expression does not prevent craniofacial malformation induced by activation of AhR during zebrafish development . This demonstrates that even though induction of Cyp1a1 is an indicator of AhR pathway activation, it is not the key target of the pathway mediating the effects on craniofacial skeletal formation.
Among the other AhR downstream targets which could be involved in mediating the craniofacial effects (Additional file 1: Table S1), we found 8 more genes showing benthic–limnetic differential expression over the examined developmental period (Fig. 5). Three of the genes, Apaf1, Cfl1 and Foxq1, might be of importance for the development of the craniofacial characteristics induced by AhR pathway activity. Apaf1 is an evolutionarily conserved cytosolic protein with a critical role in regulation of developmental apoptosis in mammals  and we found that its expression is higher in developing heads of limnetic morphs. A non-functional Apaf1 mutant in mice displays defective craniofacial development through altered regulation of hedgehog (Hh) signalling . The Hh pathway itself is known to be a key driver for adaptive variation of craniofacial skeletal structures in cichlids . In mammalian cells, the expression of Apaf1 was shown to be inhibited by overexpression of Ahr through a complex formed by AhR and E2f1 which binds to the Apaf1 promoter at a region containing E2f1 binding site, but no AhR binding sites . In general, AhR can act as a co-repressor of E2f-dependent transcription, and this is particularly interesting because binding sites for E2f were significantly enriched in our TF overrepresentation analysis .
Cfl1 encodes a protein (cofilin-1, non-muscle) that plays a role in the regulation of cell morphology and cytoskeletal organization by affecting the polymerization of actin . Activation of the AhR pathway can induce the expression of Cfl1 . Moreover, loss of function mutations as well as knock-down of Cfl1 in zebrafish result in morphological changes in the lower jaw and pharyngeal arches . Our study showed that expression of Cfl1 was consistently higher in developing heads of the benthic morphs and its expression correlated negatively with Apaf1. Moreover, WISH analysis showed clear differences in the spatial expression pattern between the morphotypes, i.e. in the frontonasal region and in components of the lower jaw and pharyngeal arches (Fig. 7).
In zebrafish, an isoform of the transcription factor Foxq1 (Foxq1b) has been reported to be induced by activation of Ahr2 and its expression was limited to the jaw primordium . Our results show higher expression of Foxq1 in developing heads of benthic morphs and strong negative expression correlation with Apaf1 (Figs. 5, 6a). We also identified differences in levels and spatial patterns of expression for Foxq1 between contrasting morphs in regions limited to ventral craniofacial structures, where it overlaps with the expression of Ahr2b, Apaf1, and Cfl1 (Fig. 7). Taken together, the transcriptional dynamics of Apaf1, Cfl1 and Foxq1 indicate higher AhR activity in benthic morphs and suggest a role for these three genes in divergent craniofacial morphogenesis in Arctic charr.
The other 5 AhR-regulated genes tested in this study, Cldn4, Jup, Mvp, Scin and Sult6b1, were found to be more highly expressed in benthic morphotypes (Fig. 5). Furthermore, most of these genes showed positive expression correlation with Ahr2b suggesting Ahr2b-dependent regulation. A junction plakoglobin gene, Jup, encodes a protein involved in cadherin-mediated intercellular communication . In mammalian cells, Jup shows an interesting biphasic transcriptional response to AhR activity . While high doses of AhR pathway agonists repressed Jup expression, a low dose could induce Jup expression . Therefore, the increased expression of Jup in developing heads of benthic morphotypes might indicate moderate AhR pathway activity. Another interesting gene, Scin (Adseverin), was already shown in a previous transcriptome analysis to be among the top differentially expressed genes between two contrasting morphs . Scin plays a role in rearranging the actin cytoskeleton, chondrocyte differentiation and in skeletal formation [101, 102]. In mice, Scin has been shown to be a direct target of the AhR pathway . Additional studies are required to determine whether the genes found in this study have role in phenotypic variation of vertebrate craniofacial morphogenesis and whether and to what extent their transcription is regulated by the AhR pathway during skeletal development.
The differential transcriptional signatures of the selected AhR target genes clearly correlate with the differences in craniofacial development between charr morphotypes. However, further studies are required to differentiate between expression dynamics of the paralogues of each AhR target gene to identify the potential paralogue-specific response to the pathway. The quantified expression differences are most likely caused by genetic differences that affect regulators (TF’s, miRNAs, translation regulators or cis-elements) of the AhR pathway or parallel pathways. Can such differences in the developmental circuitry of craniofacial development play a role in the evolution of the charr morphs? Phenotypes and alleles of developmental genes can be influenced by genetic background [104, 105]. An interesting and highly relevant example is the fact that different inbred strains of mice display differential response to AhR-mediated effects on mandible development . The morphs studied here all (except AC) exist in sympatry in Lake Thingvallavatn. Coalescent simulations involving PL and SB charr from the lake suggest a scenario of rapid divergence in allopatry followed by very slow (large populations and slow drift) divergence in sympatry and very low gene flow among the morphs . Although the nature of the genetic separation (and possibly reproductive barriers) is unknown, our data on craniofacial development in hybrids of PL and SB charr suggested developmental incompatibilities resulting in smaller heads and narrowing of the mouth and pharyngeal tract in the hybrid offspring (Kapralova et al., unpublished data). This could reduce the fitness of hybrids (e.g. at the start of exogenous feeding), and lead to strong selection against hybrids. In this respect, it is tempting to speculate that the initial, rapid divergence processes postulated could involve changes in key developmental pathways of craniofacial development, possibly the AhR pathway, resulting in developmental incompatibility of hybrids, a situation that would select for further reproductive isolation during the sympatric phase.
In this study, we investigate the molecular mechanism underlying craniofacial divergence in the highly polymorphic Arctic charr of Lake Thingvallavatn (Iceland). We have found a network of co-expressed genes with higher expression in limnetic than benthic morphotypes during early stages of craniofacial development. Key members of the network and their genetic interactions are conserved across vertebrate species. Searching for predicted upstream TFs regulating the network, we identified a receptor of the AhR pathway, Ahr2b and found a set of AhR-regulated genes to be differentially expressed between the morphotypes. We also confirmed an overlapping expression pattern of Ahr2b and AhR target genes in craniofacial structures of Arctic charr embryos. Taken together, this study suggests the AhR pathway as a key modulator of transcriptional differences along the benthic–limnetic axis of craniofacial development in Arctic charr. Considering the conserved nature of the network, it is likely to have a much broader relevance in the early development of craniofacial structures in vertebrates.
aquaculture limnetic-like fish stock
aryl hydrocarbon receptor pathway
large benthivorous charr
relative expression quantity
small benthivorous charr
- τ s :
tau-somite relative age
EPA designed and performed most experiments, conducted data analysis and drafted the manuscript. SSSt assisted with literature studies, selection of gene candidates, design of primers and performed some qPCR experiments. AP assisted in statistical data analysis. VHM set up in situ hybridization experiments. AP, SRF, SSSn, VHM and ZOJ designed the study, acquired funding, interpreted the data and co-wrote the manuscript. All authors read and approved the final manuscript.
This project was supported by The Icelandic Centre for Research (RANNIS/IRF, Grant 100204), The University of Iceland Research Fund and the Eimskip University Fund. The authors thank Bjarni K Kristjánsson, Einar Svavarsson, Kalina H. Kapralova and Soizic Le Deuff for their assistance with sampling the parents, setting up crosses, maintenance and sampling of the embryos and experimental advice and discussion. The authors also thank Jóhannes Gudbrandsson for providing R-code for cluster analysis of gene expression data, statistical advice and helpful discussions. Finally, we thank Eggert Pétursson for permitting us to use his drawings of Arctic charr heads.
Compliance with ethical guidelines
Competing interests The authors declare that they have no competing interests.
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