The development of the vertebrate face during embryogenesis requires the integration of gene regulatory programs and signaling interactions across different tissue layers to regulate normal growth and morphogenesis (Chai and Maxson, 2006; Dixon et al., 2011). The bulk of the face is derived from neural crest cells (NCCs), which migrate into the nascent mandibular, maxillary, and frontonasal facial prominences. Recent studies have indicated the cranial NCCs (CNCCs), residing within distinct facial prominences, are molecularly similar, genetically poised, and awaiting additional signaling information for their continued development (Minoux et al., 2017; Minoux and Rijli, 2010). These critical signals are provided by surrounding and adjacent tissues, especially the forebrain, endoderm, and ectoderm (Le Douarin et al., 2004). With respect to the ectoderm, studies in chick have indicated the presence of a frontonasal ectodermal zone, defined by the juxtaposition of Fgf8 and Shh expressing domains, that can direct facial outgrowth and patterning (Hu and Marcucio, 2009; Hu et al., 2003). The ectoderm is also a critical source of Wnt signaling that is required for continued facial outgrowth and patterning, exemplified by the lack of almost all craniofacial structures arising when Wls (Gpr177) is removed from the facial ectoderm (Goodnough et al., 2014; Reynolds et al., 2019). Further evidence for an essential role of the ectoderm in craniofacial development comes from genetic analysis of pathology associated with human syndromic orofacial clefting. Specifically, mutations in IRF6 (Kondo et al., 2002) and GRHL3 (Peyrard-Janvid et al., 2014) are associated with van der Woude Syndrome, while TRP63 mutations result in ectodermal dysplasias with associated facial clefting (Celli et al., 1999). Notably, all three of these human genes encode transcription factors which exhibit much stronger expression in the facial ectoderm than in the underlying neural crest (Hooper et al., 2020; Leach et al., 2017). Studies of mouse facial dysmorphology have also shown the importance of additional genes with biased expression in the ectoderm—including Sfn, Jag2, Wnt9b, and Esrp1—that regulate differentiation, signaling, and splicing (Bebee et al., 2015; Jiang et al., 1998; Jin et al., 2012; Lee et al., 2013; Lee et al., 2020; Richardson et al., 2006). Indeed, the interplay between surface ectoderm and underlying NCCs provides a molecular platform for the craniofacial diversity apparent within the vertebrate clade, but also serves as a system which is frequently disrupted to cause human craniofacial birth defects. Therefore, identifying the regulatory mechanisms and factors involved in coordinating NCC:ectoderm interactions is a prerequisite for uncovering the molecular nodes susceptible to perturbation.

The AP-2 transcription factor family represents an intriguing group of regulatory molecules with strong links to ectodermal development (Eckert et al., 2005). Indeed, previous analyses have indicated that AP-2 genes may be an ancestral transcriptional regulator of ectoderm development in chordates predating the development of the neural crest in the cephalochordate Amphioxus and the ascidian Ciona (Imai et al., 2017; Meulemans and Bronner-Fraser, 2002; Meulemans and Bronner-Fraser, 2004). Subsequently, it has been postulated that this gene family has been co-opted into the regulatory network required for neural crest development in the vertebrates, where it may serve as one of the master regulators of this lineage (Meulemans and Bronner-Fraser, 2002; Meulemans and Bronner-Fraser, 2004; Van Otterloo et al., 2012). Therefore, in vertebrates, AP-2 family expression is often observed in both the non-neural ectoderm as well as the neural crest. Amphioxus possesses a single AP-2 gene, but in mammals such as mouse and human there are five family members, Tfap2a-e encoding the proteins AP-2α-ε, respectively (Eckert et al., 2005; Meulemans and Bronner-Fraser, 2002). All mammalian AP-2 proteins have very similar DNA sequence preferences and bind as dimers to a consensus motif GCCNNNGGC, except for AP-2δ which is the least conserved family member (Badis et al., 2009; Williams and Tjian, 1991; Zhao et al., 2001). Amongst these five genes, Tfap2a and Tfap2b show the highest levels of expression in the developing mouse embryonic facial tissues with lower levels of Tfap2c and essentially undetectable transcripts from Tfap2d and Tfap2e (Hooper et al., 2020; Van Otterloo et al., 2018). Importantly, mutations in human TFAP2A and TFAP2B, are also linked to the human conditions Branchio-Oculo-Facial Syndrome (Milunsky et al., 2008) and Char Syndrome (Satoda et al., 2000) respectively, conditions which both have a craniofacial component. TFAP2A has also been linked to non-syndromic orofacial clefting (MIM 119530) (Davies et al., 1995; Davies et al., 2004).

Previous single mouse knockout studies have indicated that the loss of Tfap2a has the most significant effect on craniofacial development with most of the upper face absent as well as split mandible and tongue (Schorle et al., 1996; Zhang et al., 1996). Tfap2b knockouts do not have gross morphological defects associated with craniofacial development (Hong et al., 2008; Moser et al., 1997; Zhao et al., 2011), nor do pertinent knockouts of any of the three other AP-2 genes (Feng et al., 2009; Guttormsen et al., 2008; Hesse et al., 2011). We have further investigated the tissue specific requirements for Tfap2a in face formation and determined that its loss in the neural crest resulted in cleft palate, but otherwise only minor defects in the development of the facial skeleton (Brewer et al., 2004). Next, we investigated whether the co-expression of Tfap2b might compensate for the loss of Tfap2a alone by deriving mice lacking both genes in NCCs. Although these NCC double knockout mice had more severe craniofacial defects, including a split upper face and mandible, the phenotype was still less severe than that observed with the complete loss of Tfap2a alone (Van Otterloo et al., 2018; Zhang et al., 1996). In contrast, targeting Tfap2a in the surface ectoderm in the region of the face associated with the lens placode causes a mild form of orofacial clefting (Pontoriero et al., 2008). These findings suggested that the ectoderm may be an additional major site of Tfap2a action during mouse facial development, and by analogy with the NCC studies, that the phenotype could be exacerbated by the additional loss of Tfap2b.

Therefore, here we have assessed how craniofacial development is affected upon simultaneous removal of Tfap2a and Tfap2b in the embryonic ectoderm using the Cre transgene, Crect, which is expressed from E8.5 onwards throughout this tissue layer. Our results show that the expression of these two AP-2 proteins in the ectoderm has a profound effect on the underlying NCC-derived craniofacial skeleton and strengthens the association between the AP-2 family and ectodermal development and function. Furthermore, we examined how the loss of these two AP-2 transcription factors impacted the ectodermal craniofacial gene regulatory network by studying changes in chromatin accessibility and gene expression between control and mutant mice. These studies reveal critical targets of AP-2 within the facial ectoderm, especially WNT pathway genes, and further indicate the necessity of appropriate ectodermal:mesenchymal communication for growth, morphogenesis, and patterning of the vertebrate face.

Development of the vertebrate head requires critical regulatory interactions between various tissue layers, particularly the ectoderm and underlying neural crest derived mesenchyme. Here, we show that AP-2 transcription factors are an essential component of a mouse early embryonic ectoderm GRN directing growth and morphogenesis of the underlying facial prominence tissues. Specifically, combined conditional loss of the two most highly expressed members of the family within the ectoderm, Tfap2a and Tfap2b, results in a failure of the facial prominences to meet and fuse productively. Thus, the mandibular processes fail to meet at the midline, resulting in a wide separation between the two halves of the lower jaw and a bifid tongue. In the upper face, the maxillary, and lateral and medial nasal prominences fail to align at the lambdoid junction, resulting in an extensive bilateral cleft and significant midfacial dysmorphology. In addition to the orofacial clefting phenotypes, there was also loss of the normal hinge region between the mandible and maxilla resulting in syngnathia, and a duplication of Meckel’s cartilage. Overall, the data indicate that appropriate growth, morphogenesis, and patterning of the facial prominences are all severely disrupted. The finding that AP-2α and AP-2ß work redundantly in the facial ectoderm complements studies showing that they can also work together within the cranial neural crest to control facial development (Van Otterloo et al., 2018). In these previous studies, the neural crest specific deletion of these factors resulted in a different type of orofacial cleft—an upper midfacial cleft—but in common with the EDKO mutants also caused syngnathia. The observations that AP-2α and AP-2ß have distinct as well as overlapping functions with both the neural crest and ectoderm for mouse facial development also inform both human facial clefting genetics and evolutionary biology. With respect to humans, TFAP2A mutations are associated with Branchio-Oculo-Facial Syndrome (MIM, 113620), while TFAP2B is mutated in Char Syndrome (MIM, 169100) (Satoda et al., 2000). Although both syndromes have craniofacial components to their pathology, including changes to the nasal bridge and the position of the external ears, only mutations in TFAP2A are associated with orofacial clefting, usually lateral. These findings support a more significant role for TFAP2A in influencing orofacial clefting in both mouse and human and suggest that it is the reduction of AP-2α function in the ectoderm—rather than the NCC —that is associated with this human birth defect.

In the context of chordate evolution, the prevailing hypothesis is that AP-2 has an ‘ancestral’ role within the non-neural ectoderm followed by an ‘evolved’ role within the neural crest cell lineage of vertebrates (Meulemans and Bronner-Fraser, 2002; Van Otterloo et al., 2012). The current studies further support that AP-2 proteins have critical roles within the embryonic ectoderm that have been conserved from cephalochordates and tunicates through to mammals. Alongside established roles for AP-2 transcription factors in NCCs (Brewer et al., 2004; Martino et al., 2016; Prescott et al., 2015; Van Otterloo et al., 2018), these observations raise the possibility that there may be a coordinated and complex interplay between AP-2 activity in the two tissue layers that has been conserved during evolution. The combined function of the two AP-2 factors in craniofacial development also reflects the more severe pathology resulting from the loss of more than one AP-2 gene that has been documented in other mouse developmental systems including the eye, nervous system, and skin (Hicks et al., 2018; Schmidt et al., 2011; Wang et al., 2008; Zainolabidin et al., 2017). The propensity of the AP-2 proteins to act in concert has also been observed in additional vertebrate species, particularly in the chick and zebrafish, where loss of more than one gene uncovers joint functions in neural crest, face, and melanocyte development (Hoffman et al., 2007; Knight et al., 2005; Li and Cornell, 2007; Rothstein and Simoes-Costa, 2020; Van Otterloo et al., 2010). Notably, in the zebrafish, previous studies have documented an interaction between AP-2α and AP-2ß during cranial NCC development (Knight et al., 2005). Unlike in the mouse, AP-2ß’s role was confined to the surface ectoderm, based on gene expression and transplant experiments. However, more recent single-cell transcriptome profiling has identified tfap2b expression in the zebrafish cranial neural crest (Mitchell et al., 2021), suggesting features between these models (i.e. zebrafish and mouse) may be more conserved than previously thought.

The joint function of these AP-2 proteins in controlling specific aspects of gene expression presumably reflects the similar consensus sequence recognized by all family members (Badis et al., 2009; Bosher et al., 1996; Williams and Tjian, 1991). Thus, the absence of AP-2ß alone may not cause major developmental issues in mouse facial development due to the ability of the remaining AP-2α protein to bind and regulate shared critical genes. However, loss of both proteins would lower the amount of functional AP-2 protein available for normal gene regulation. The hypothesis that particular levels of AP-2 are required for achieving critical thresholds of gene activity is also supported by the different phenotypes uncovered by the loss of particular Tfap2a and Tfap2b allelic combinations. Thus, while the loss of one allele of Tfap2a—or both alleles of Tfap2b—in the ectoderm is tolerated in the context of facial development, the combined loss of all three of these four alleles is not, and the phenotypes become more severe when all four alleles are defective. We note that this phenomenon was also observed when these genes were targeted in the neural crest (Van Otterloo et al., 2018). In both the NCCs and ectoderm the role of AP-2α seemed to be more significant than AP-2ß based on the phenotypes observed—since the presence of one functional allele of Tfap2a resulted in less severe pathology than the converse where only a single productive Tfap2b allele was expressed. The reasons behind the more prominent function of AP-2α in these systems remains unclear, especially since the two proteins are over 70% identical and bind to the same DNA recognition sequences. Nevertheless, it is possible that some alterations in the mRNA and/or amino acid sequence could differentially affect stability, localization, or interaction with cofactors. Alternatively, there might be subtle differences in the timing, distribution, or levels of functional AP-2α and AP-2ß protein in these tissues that account for the changes in susceptibility to pathology. Further studies will be needed to determine how the consequence of Tfap2a loss is greater than Tfap2b.

One notable observation, though, is that no unique and irreplaceable function exists for any AP-2α/ß heterodimers in the mouse ectoderm or neural crest. This conclusion is based on the finding that loss of Tfap2b—a situation that would impact both AP-2ß homodimers and AP-2α/ß heterodimers—does not impact facial development in these experiments. Finally, the sensitivity of facial development to changes in the allelic dosage of the AP-2 proteins makes this gene family a potential contributor to the evolution of facial shape. Indeed, this conjecture is supported by studies comparing genetic and morphological changes in different threespine stickleback (Erickson et al., 2018) and Arctic charr (Ahi et al., 2015) populations adapted to diverse environmental conditions, as well as by comparative studies of IPS-derived cranial neural crest cells from human and chimp, which suggest that changes in AP-2 expression and/or gene targets correlate with facial shape changes (Prescott et al., 2015).

The severe EDKO phenotypes also indicated that the presence or absence of these AP-2 transcription factors in the ectoderm must have a profound influence on chromatin dynamics and gene expression. To probe this in depth, ATAC-seq, H3K4me3 ChIP-seq, and RNAseq were performed on control samples derived from the embryonic mouse face, to correlate respectively chromatin accessibility, active promoter marks, and gene expression. These datasets revealed chromatin signatures that were tissue generic as well as a subset that were specific for the E11.5 facial ectoderm with the latter enriched for P53/P63/P73, AP-2, TEAD, GRHL, and PBX binding motifs. In this respect binding motifs for P53, AP-2, and TEAD family members have previously been found associated with ectodermal-specific gene regulatory pathways in embryonic skin (Fan et al., 2018; Wang et al., 2006; Wang et al., 2008; Yuan et al., 2020). Notably, our studies extend and refine the previous genome-wide analysis of embryonic skin conducted by Fan et al., 2018 by focusing on the E11.5 facial ectoderm, enabling the detection of additional binding motifs for GRHL and PBX TF family members that are critical craniofacial patterning genes. We complemented the analysis of control samples by performing equivalent ATAC-seq and RNAseq studies on EDKO facial ectoderm or whole facial prominences, respectively. Deletion of these two transcription factors led to a significant (5%) genome-wide loss of chromatin accessibility that was centered on AP-2 consensus motifs, particularly in potential distal enhancer elements. Despite changes in the accessibility of AP-2 binding sites, motifs for P53 and TEAD family members were still highly enriched in the EDKO mutant samples. These observations provide support for previous ATAC-seq analysis of deltaNp63 mutants which hypothesized that the AP-2 and p63 programs may function independently at the protein level to regulate chromatin accessibility in embryonic ectoderm (Fan et al., 2018). Many of the genes linked to AP-2 binding motifs were associated with annotations aligned to skin development, such as keratins, cadherins, and gap junction proteins. However, further analysis of the gene list also revealed an evolutionary conserved group of AP-2-binding motifs connected with WNT-related genes, many associated with craniofacial development.

A strong link between AP-2 function, skin development, and WNT pathway expression was also detected in the RNAseq datasets. Changes between control and EDKO mutants in the expression of various keratin genes as well Gjb6, Trp63, Grhl3, and Lin28a suggest a failure or delay in appropriate skin differentiation in the latter embryos. Further, loss of AP-2α/ß caused a significant reduction in expression of many Wnt ligands within the facial ectoderm including Wnt3, Wnt6, Wnt9b, and Wnt10a. Importantly, these four Wnt genes have been associated with human orofacial clefting (Reynolds et al., 2019), and alterations of Wnt9b also cause mouse CL/P (Juriloff et al., 2005; Juriloff et al., 2006). The reduced output of WNT signaling from the ectoderm was matched by a reduction of Axin2-LacZ reporter expression in the underlying mesenchyme, and there were also multiple changes in additional WNT components in the mesenchyme suggesting that loss of ectodermal AP-2 expression has significantly disrupted the function of this pathway throughout the developing face. Note that, although Wnt ligand expression is reduced in the ectoderm of EDKO mutants, it is not completely lost. Therefore, the facial pathology is not as severe as that observed with the ectodermal loss of Wls, a gene required for WNT ligand modification and secretion, in which the majority of the face is absent (Goodnough et al., 2014). The presence of teeth in the EDKO mutants (Woodruff et al., 2021)—although abnormal in position and number—also argues against a catastrophic loss of WNT signaling within the oral ectoderm. Further studies will be required to assess how the loss of Tfap2a and Tfap2b in the ectoderm affects other structures that require ectodermal WNT function, such as hair, whiskers, and mammary buds. With respect to facial development, additional evidence for a contribution of the WNT signaling pathway to the AP-2 mutant phenotype was obtained by overexpressing Wnt1 in the EDKO mutant background, which resulted in a significant rescue of the facial dysmorphology and clefting. A previous study also indicated that ectopic Wnt1 expression could rescue CL/P caused by loss of PBX expression (Ferretti et al., 2011), suggesting either that reduced WNT signaling is a common pathogenic mechanism for clefting or that facial growth stimulated by excess WNT signaling can mitigate the defects in juxtaposition and fusion of the facial prominences. Note that normal facial morphology was not fully recapitulated in the EDKO rescue experiments, possibly reflecting that the timing and level of Wnt1 expression was not optimal. We also note that Wnt1 overexpression did not affect clefting of the lower jaw in EAKO and EDKO mice, nor is the expression of genes previously linked with syngnathia and jaw-joint defects, such as Foxc1, Six1, Bmp4, Fgf8, or Dlx (Jeong et al., 2008; Inman et al., 2013; He et al., 2014; Achilleos and Trainor, 2015; Liu et al., 2019; Abe et al., 2021) family members significantly changed in the EDKO model. Therefore, further analysis will be required to uncover the role of ectodermal Tfap2 expression in development of the syngnathia and other mandible defects. Indeed, our data shows that AP-2 directs additional ectodermal programs that also contribute to face formation—including IRX and IRF TF expression—as well as CXCL, EDN, FGF, and NOTCH signaling that presumably contribute to the overall pathology of the EAKO and EDKO mice. Importantly, IRF6—a gene involved in orofacial clefting (Kondo et al., 2002; Zucchero et al., 2004)—has previously been identified as a critical AP-2 target. Studies in human have shown that a polymorphism in an upstream enhancer element either generates or disrupts a binding site for AP-2 proteins, with the latter variant increasing the risk for orofacial clefting (Rahimov et al., 2008). This enhancer is conserved in the mouse, and its accessibility is altered in the EDKO mutant. Further, the expression of Irf6 is also reduced in the EDKO mutants (Supplementary file 3), correlating with the loss of AP-2 binding, and providing a further pathway that might contribute to the overall phenotype. In summary, the combination of ATAC-seq, ChIP-Seq, and expression analyses highlight critical genes that are impacted by loss of AP-2 transcription factors. These data greatly expand our understanding of the gene regulatory circuits occurring in the ectoderm that regulate facial development and underscore a critical role for AP-2α and AP-2ß in controlling appropriate genome access as well as gene expression.

Sequencing data has been deposited in the Gene Expression Omnibus under accession code GSE199342.

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Author details

1. Eric Van Otterloo

   1. Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, United States
   2. Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, United States
   3. Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, United States
   4. Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing

   For correspondence

   eric-vanotterloo@uiowa.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-5958-5742

2. Isaac Milanda

   Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, United States

   Contribution

   Data curation, Formal analysis, Investigation

   Competing interests

   No competing interests declared

3. Hamish Pike

   Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, United States

   Contribution

   Formal analysis, Investigation

   Competing interests

   No competing interests declared

4. Jamie A Thompson

   1. Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, United States
   2. Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, United States

   Contribution

   Data curation, Formal analysis, Investigation, Writing – review and editing

   Competing interests

   No competing interests declared

5. Hong Li

   Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, United States

   Contribution

   Formal analysis, Investigation

   Competing interests

   No competing interests declared

6. Kenneth L Jones

   Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States

   Present address

   Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, United States

   Contribution

   Formal analysis, Resources, Software

   Competing interests

   No competing interests declared

7. Trevor Williams

   1. Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
   2. Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
   3. Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Writing – original draft, Writing – review and editing

   For correspondence

   trevor.williams@cuanschutz.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-2416-4603

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