Exploring the effects of gene dosage on mandible shape in mice as a model for studying the genetic basis of natural variation

Advance in candidate genes in mandibular retrognathism: A systematic review

OBJECTIVE

This research aims to dissect the polygenic nature of non-syndromic mandibular retrognathism (MR) and to better understand the genetic underpinnings of MR, with a particular focus on the role of ethnic diversity in influencing genetic predispositions.

METHODS

A comprehensive systematic review was conducted on MR. Electronic databases such as PubMed and Google Scholar were employed, utilizing terms like 'mandibular', 'retrognathism', 'gene', and 'genetic'. This study strictly adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework.

RESULTS

Ten genetic studies were identified that satisfied the eligibility criteria, involving 1010 participants. Variations in candidate genes were reported across different populations, including myosin 1 H (MYO1H), matrilin 1 (MATN1), a disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9), bone morphogenetic protein 2 (BMP2), parathyroid hormone (PTH), the vitamin-D related genes: vitamin D receptor (VDR), cytochrome P450 family 24 subfamily A member 1 (CYP24A1), and cytochrome P450 family 27 subfamily B member 1 (CYP27B1), collagen type II alpha 1 chain (COL2A1), transforming growth factor-β (TGF-β), TGF-β receptor 2 (TGFBR2), epidermal growth factor (EGF), and EGF receptor gene (EGFR).

CONCLUSION

These findings shed light on the role of genetic factors in MR. Future studies should adopt a multicentric approach to expand sample sizes and enhance the analysis of genetic variants associated with MR.

Leveraging Descriptor Learning and Functional Map-based Shape Matching for Automatic Landmark Acquisition

Geometric morphometrics is widely employed across the biological sciences for the quantification of morphological traits. However, the scalability of these methods to large datasets is hampered by the requisite placement of landmarks, which can be laborious and time consuming if done manually. Additionally, the selected landmarks embody a particular hypothesis regarding the critical geometry pertinent to the biological inquiry at hand. Modifying this hypothesis lacks flexibility, necessitating the acquisition of an entirely new set of landmarks on the entire dataset to reflect any theoretical adjustments. In our research, we investigate the precision and accuracy of landmarks derived from the comprehensive set of functional correspondences acquired through the functional map framework of geometry processing. We use a deep functional map network to learn shape descriptors that effectively yield functional map-based and point-to-point correspondences between the specimens in our dataset. We then interrogate these maps to identify corresponding landmarks given manually placed landmarks from the entire dataset. We assess our method by automating the landmarking process on a dataset comprising mandibles from various rodent species, comparing its efficacy against MALPACA, a cutting-edge technique for automatic landmark placement. Compared to MALPACA, our model is notably faster and maintains competitive accuracy. The Root Mean Square Error (RMSE) analysis reveals that while MALPACA generally exhibits the lowest RMSE, our models perform comparably, especially with smaller training datasets, suggesting strong generalizability. Visual evaluations confirm the precision of our landmark placements, with deviations remaining within an acceptable range. These findings underscore the potential of unsupervised learning models in anatomical landmark placement, providing a viable and efficient alternative to traditional methods.

Effects of obesity on the rat incisor enamel and dentine thickness, as well as on the hemimandible shape over generations

Obesity has several effects on the general body metabolism. However, little is known about the impact of obesity on the growth and shape of mineralized tissues like mandibles and teeth, as well as if it effects are passed down from generation to next. Therefore, in this study, we aimed to evaluate, over nine generations using the consanguineous mating (inbreeding), the effect of the obesity condition produced by the reduction in the number of rats per litter during the lactation period on the hemimandible shape, dentine, and enamel of the rat incisor. Litters were reduced to two males and two females after birth, and were consanguinity mated in adulthood for nine generations. For all evaluations performed in this investigation, only males were used. The control group was formed by a non-consanguineous litter containing eight males. The parameters evaluated were food consumption, body weight, Lee Index, and bone density of the hemimandible bone. Incisor enamel and dentine thickness were also evaluated. The hemimandible shape was evaluated using geometric morphometry. The results show a significant and progressive increase in food intake, Lee Index, body weight, hemimandible weight, and enamel thickness, and a decrease in dentine thickness. The linear measurements of the length of the ramus ascending hemimandibular segment were found to be shorter, while its height was increased. In contrast, the geometric morphometry shows that the general hemimandible shape changed over the consanguineous obesity generations. We conclude that over generations, obesity increases and maintains the parameters evaluated with significant changes in hemimandible shape as well as in the dimensions of enamel and dentine of incisors, suggesting that enamel and dentine could be used as phenotype biomarkers to detect changes in tooth and craniofacial development related to obesity effects.

One Hundred Years of Gene Balance: How Stoichiometric Issues Affect Gene Expression, Genome Evolution, and Quantitative Traits

A century ago experiments with the flowering plant Datura stramonium and the fruit fly Drosophila melanogaster revealed that adding an extra chromosome to a karyotype was much more detrimental than adding a whole set of chromosomes. This phenomenon was referred to as gene balance and has been recapitulated across eukaryotic species. Here, we retrace some developments in this field. Molecular studies suggest that the basis of balance involves stoichiometric relationships of multi-component interactions. This concept has implication for the mechanisms controlling gene expression, genome evolution, sex chromosome evolution/dosage compensation, speciation mechanisms, and the underlying genetics of quantitative traits.

Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize

The phenotypic consequences of the addition or subtraction of part of a chromosome is more severe than changing the dosage of the whole genome. By crossing diploid trisomies to a haploid inducer, we identified 17 distal segmental haploid disomies that cover ∼80% of the maize genome. Disomic haploids provide a level of genomic imbalance that is not ordinarily achievable in multicellular eukaryotes, allowing the impact to be stronger and more easily studied. Transcriptome size estimates revealed that a few disomies inversely modulate most of the transcriptome. Based on RNA sequencing, the expression levels of genes located on the varied chromosome arms (cis) in disomies ranged from being proportional to chromosomal dosage (dosage effect) to showing dosage compensation with no expression change with dosage. For genes not located on the varied chromosome arm (trans), an obvious trans-acting effect can be observed, with the majority showing a decreased modulation (inverse effect). The extent of dosage compensation of varied cis genes correlates with the extent of trans inverse effects across the 17 genomic regions studied. The results also have implications for the role of stoichiometry in gene expression, the control of quantitative traits, and the evolution of dosage-sensitive genes.

An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects

We are motivated by biological studies intended to understand global gene expression fold change. Biologists have generally adopted a fixed cutoff to determine the significance of fold changes in gene expression studies (e.g. by using an observed fold change equal to two as a fixed threshold). Scientists can also use a t-test or a modified differential expression test to assess the significance of fold changes. However, these methods either fail to take advantage of the high dimensionality of gene expression data or fail to test fold change directly. Our research develops a new empirical Bayesian approach to substantially improve the power and accuracy of fold-change detection. Specifically, we more accurately estimate gene-wise error variation in the log of fold change. We then adopt a t-test with adjusted degrees of freedom for significance assessment. We apply our method to a dosage study in Arabidopsis and a Down syndrome study in humans to illustrate the utility of our approach. We also present a simulation study based on real datasets to demonstrate the accuracy of our method relative to error variance estimation and power in fold-change detection. Our developed R package with a detailed user manual is publicly available on GitHub at https://github.com/cuiyingbeicheng/Foldseq.

GmKIX8-1 regulates organ size in soybean and is the causative gene for the major seed weight QTL qSw17-1

Seed weight is one of the most important agronomic traits in soybean for yield improvement and food production. Several quantitative trait loci (QTLs) associated with the trait have been identified in soybean. However, the genes underlying the QTLs and their functions remain largely unknown. Using forward genetic methods and CRISPR/Cas9 gene editing, we identified and characterized the role of GmKIX8-1 in the control of organ size in soybean. GmKIX8-1 belongs to a family of KIX domain-containing proteins that negatively regulate cell proliferation in plants. Consistent with this predicted function, we found that loss-of-function GmKIX8-1 mutants showed a significant increase in the size of aerial plant organs, such as seeds and leaves. Likewise, the increase in organ size is due to increased cell proliferation, rather than cell expansion, and increased expression of CYCLIN D3;1-10. Lastly, molecular analysis of soybean germplasms harboring the qSw17-1 QTL for the big-seeded phenotype indicated that reduced expression of GmKIX8-1 is the genetic basis of the qSw17-1 phenotype.

Geographical variation in Eurasian red squirrel (Sciurus vulgaris L., 1758) mandibles and the issue of subspecies-level organization: a failure of history?

Sciurus vulgaris is a widespread, highly polytypic tree squirrel species, under which a large number of subspecies have been described. This study tests the robustness of the current subspecific classification by using geometric morphometrics to quantify morphological variation in mandible shape, along with canonical variates analysis to test hypotheses of morphological distinctiveness. Patterns of mandible allometry were examined in eight out of 16 currently recognized subspecies. The significance of the discriminate functions was tested statistically, and the iterative jackknife procedure was applied to evaluate stability of the subspecies-specific discriminant functions. Applying criteria that focus on shape diagnosability, rather than mean group differences, indicates that most regional subspecific groupings show intergradations and continuity in mandible shape and size and that allometric effects on mandible shape are negligible. Evidence of a distinct subspecies confined to the Iberian Peninsula (Sciurus vulgaris infuscatus) and a discrete group originating from an extinct, 19th century population in Dorset, UK were identified based on these mandibular data. All other regional subspecific groupings were not diagnosably different. These results suggest that most red squirrel subspecies might represent non-diagnosable morphological variants whose taxonomic validity seems doubtful. More generally, our results highlight the importance of applying objective, quantitative and reproducible criteria to the issue of subspecies delimitation.

Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa

Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.

Upper jaw development in the absence of teeth: New insights for craniodental evo-devo integration

In p63-null mice (p63^-/- ), teeth fail to form but the mandible forms normally; conversely, the upper jaw skeleton is malformed. Here we explored whether lack of dental tissues contributed to midfacial dysmorphologies in p63^-/- mice by testing if facial prominence defects appeared before odontogenesis failed. We also investigated gene dose effects by testing if one wild type (WT) p63 allele (p63^+/- ) was sufficient for normal upper jaw skeleton formation. We micro-CT scanned PFA-fixed p63^-/- , p63^+/- , and WT (p63^+/+ ) adult and embryonic mice aged E10-E14. Next, we landmarked mandibular (MdP), maxillary (MxP) and nasal prominences (NPs), and facial bones. 3D landmark data were assessed using Principal Component, Canonical Variate, Partial Least Squares, and other statistical analyses. The p63^-/- embryos showed MxP and NP malformations by E12, despite the presence of dental tissues. MdP shape was comparable among p63^-/- , p63^+/- , and p63^+/+ embryos. Upper jaw shape was comparable between p63^+/+ and p63^+/- adults. The upper jaw and its dentition both require p63 signaling, but not each other's presence, to form properly. One WT p63 allele enables normal midfacial morphogenesis; gene dose may be a target for jaw macroevolution. Jaw-specific genetic mechanisms likely integrate the evo-devo of dentitions with upper versus lower jaws.

Linkage mapping of yeast cross protection connects gene expression variation to a higher-order organismal trait

Gene expression variation is extensive in nature, and is hypothesized to play a major role in shaping phenotypic diversity. However, connecting differences in gene expression across individuals to higher-order organismal traits is not trivial. In many cases, gene expression variation may be evolutionarily neutral, and in other cases expression variation may only affect phenotype under specific conditions. To understand connections between gene expression variation and stress defense phenotypes, we have been leveraging extensive natural variation in the gene expression response to acute ethanol in laboratory and wild Saccharomyces cerevisiae strains. Previous work found that the genetic architecture underlying these expression differences included dozens of “hotspot” loci that affected many transcripts in trans. In the present study, we provide new evidence that one of these expression QTL hotspot loci affects natural variation in one particular stress defense phenotype—ethanol-induced cross protection against severe doses of H₂O₂. A major causative polymorphism is in the heme-activated transcription factor Hap1p, which we show directly impacts cross protection, but not the basal H₂O₂ resistance of unstressed cells. This provides further support that distinct cellular mechanisms underlie basal and acquired stress resistance. We also show that Hap1p-dependent cross protection relies on novel regulation of cytosolic catalase T (Ctt1p) during ethanol stress in a wild oak strain. Because ethanol accumulation precedes aerobic respiration and accompanying reactive oxygen species formation, wild strains with the ability to anticipate impending oxidative stress would likely be at an advantage. This study highlights how strategically chosen traits that better correlate with gene expression changes can improve our power to identify novel connections between gene expression variation and higher-order organismal phenotypes.

A major goal in genetics is to understand how individuals with different genetic makeups respond to their environment. Understanding these “gene-environment interactions” is important for the development of personalized medicine. For example, gene-environment interactions can explain why some people are more sensitive to certain drugs or are more likely to get certain cancers. While the underlying causes of gene-environment interactions are unclear, one possibility is that differences in gene expression across individuals are responsible. In this study, we examined that possibility using baker’s yeast as a model. We were interested in a phenomenon called acquired stress resistance, where cells exposed to a mild dose of one stress can become resistant to an otherwise lethal dose of severe stress. This response is observed in diverse organisms ranging from bacteria to humans, though the specific mechanisms governing acquisition of higher stress resistance are poorly understood. To understand the differences between yeast strains with and without the ability to acquire further stress resistance, we employed genetic mapping. We found that part of the variation in acquired stress resistance was due to sequence differences in a key regulatory protein, thus providing new insight into how different individuals respond to acute environmental change.

Cooperative interaction of BMP signalling and Foxn1 gene dosage determines the size of the functionally active thymic epithelial compartment

Thymopoiesis strictly depends on the function of the Foxn1 transcription factor that is expressed in the thymic epithelium. During embryonic development, initial expression of the Foxn1 gene is induced in the pharyngeal endoderm by mesenchyme-derived BMP4 signals. Here, by engineering a time-delayed feedback system of BMP inhibition in mouse embryos, we demonstrate that thymopoiesis irreversibly fails if Foxn1 gene expression does not occur during a defining time span in mid-gestation. We also reveal an epistatic interaction between the extent of BMP signalling and the gene dosage of Foxn1. Our findings illustrate the complexities of the early steps of thymopoiesis and indicate that sporadic forms of thymic hypoplasia in humans may result from the interaction of genes affecting the magnitude of BMP signalling and Foxn1 expression.

Detangling the evolutionary developmental integration of dentate jaws: evidence that a p63 gene network regulates odontogenesis exclusive of mandible morphogenesis

Vertebrate jaws and dentitions fit and function together, yet the genetic processes that coordinate cranial and dental morphogenesis and evolution remain poorly understood. Teeth but not jaws fail to form in the edentate p63^-/- mouse mutant, which we used here to identify genes important to odontogenesis, but not jaw morphogenesis, and that may allow dentitions to change during development and evolution without necessarily affecting the jaw skeleton. With the working hypothesis that tooth and jaw development are autonomously controlled by discreet gene regulatory networks, using gene expression microarray assays validated by quantitative reverse-transcription PCR we contrasted expression in mandibular prominences at embryonic days (E) 10-13 of mice with normal lower jaw development but either normal (p63^+/- , p63^+/+ ) or arrested (p63^-/- ) tooth development. The p63^-/- mice showed significantly different expression (fold change ≥2, ≤-2; P ≤ 0.05) of several genes. Some of these are known to help regulate odontogenesis (e.g., p63, Osr2, Cldn3/4) and/or to be targets of p63 (e.g., Jag1/2, Fgfr2); other genes have no previously reported roles in odontogenesis or the p63 pathway (e.g., Fermt1, Cbln1, Pltp, Krt8). As expected, from E10 to E13, few genes known to regulate mandible morphogenesis differed in expression between mouse strains. This study newly links several genes to odontogenesis and/or to the p63 signaling network. We propose that these genes act in a novel odontogenic network that is exclusive of lower jaw morphogenesis, and posit that this network evolved in oral, not pharyngeal, teeth.

Implications of Vertebrate Craniodental Evo-Devo for Human Oral Health

Highly processed diets eaten by postindustrial modern human populations coincide with higher frequencies of third molar impaction, malocclusion, and temporomandibular joint disorders that affect millions of people worldwide each year. Current treatments address symptoms, not causes, because the multifactorial etiologies of these three concerns mask which factors incline certain people to malocclusion, impaction, and/or joint issues. Deep scientific curiosity about the origins of jaws and dentitions continues to yield rich insights about the developmental genetic mechanisms that underpin healthy craniodental morphogenesis and integration. Mounting evidence from evolution and development (Evo-Devo) studies suggests that function is another mechanism important to healthy craniodental integration and fit. Starting as early as weaning, softer diets and thus lower bite forces appear to relax or disrupt integration of oral tissues, alter development and growth, and catalyze impaction, malocclusion, and jaw joint disorders. How developing oral tissues respond to bite forces remains poorly understood, but biomechanical feedback seems to alter balances of local bone resorption and deposition at the tooth-bone interface as well as affect tempos and amounts of facial outgrowth. Also, behavioral changes in jaw function and parafunction contribute to degeneration and pain in joint articular cartilages and masticatory muscles. The developmental genetic contribution to craniodental misfits and disorders is undeniable but still unclear; however, at present, human diet and jaw function remain important and much more actionable clinical targets. New Evo-Devo studies are needed to explain how function interfaces with craniodental phenotypic plasticity, variation, and evolvability to yield a spectrum of healthy and mismatched dentitions and jaws.

BMP signaling regulates the fate of chondro-osteoprogenitor cells in facial mesenchyme in a stage-specific manner

BACKGROUND

Lineage tracing has shown that most of the facial skeleton is derived from cranial neural crest cells. However, the local signals that influence postmigratory, neural crest-derived mesenchyme also play a major role in patterning the skeleton. Here, we study the role of BMP signaling in regulating the fate of chondro-osteoprogenitor cells in the face.

RESULTS

A single Noggin-soaked bead inserted into stage 15 chicken embryos induced an ectopic cartilage resembling the interorbital septum within the palate and other midline structures. In contrast, the same treatment in stage 20 embryos caused a loss of bones. The molecular basis for the stage-specific response to Noggin lay in the simultaneous up-regulation of SOX9 and downregulation of RUNX2 in the maxillary mesenchyme, increased cell adhesiveness as shown by N-cadherin induction around the beads and increased RA pathway gene expression. None of these changes were observed in stage 20 embryos.

CONCLUSIONS

These experiments demonstrate how slight changes in expression of growth factors such as BMPs could lead to gain or loss of cartilage in the upper jaw during vertebrate evolution. In addition, BMPs have at least two roles: one in patterning the skull and another in regulating the skeletogenic fates of neural crest-derived mesenchyme. Developmental Dynamics 245:947-962, 2016. © 2016 Wiley Periodicals, Inc.

Parallel Universes for Models of X Chromosome Dosage Compensation in Drosophila: A Review

Dosage compensation in Drosophila involves an approximately 2-fold increase in expression of the single X chromosome in males compared to the per gene expression in females with 2 X chromosomes. Two models have been considered for an explanation. One proposes that the male-specific lethal (MSL) complex that is associated with the male X chromosome brings histone modifiers to the sex chromosome to increase its expression. The other proposes that the inverse effect which results from genomic imbalance would tend to upregulate the genome approximately 2-fold, but the MSL complex sequesters histone modifiers from the autosomes to the X to mute this autosomal male-biased expression. On the X, the MSL complex must override the high level of resulting histone modifications to prevent overcompensation of the X chromosome. Each model is evaluated in terms of fitting classical genetic and recent molecular data. Potential paths toward resolving the models are suggested.

Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape?

We describe the application of high-resolution 3D microcomputed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTL responsible for variation in the mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. Despite the increasing availability of 3D imaging techniques, artificial flattening of the mandible by 2D imaging techniques seems at first an acceptable compromise for large-scale phenotyping protocols, thanks to an abundance of low-cost digital imaging systems such as microscopes or digital cameras. We evaluated the gain of information from considering explicitly this additional third dimension, and also from capturing variation on the bone surface where no precise anatomical landmark can be marked. Multivariate QTL mapping conducted with different landmark configurations (2D vs. 3D; manual vs. semilandmarks) broadly agreed with the findings of previous studies. Significantly more QTL (23) were identified and more precisely mapped when the mandible shape was captured with a large set of semilandmarks coupled with manual landmarks. It appears that finer phenotypic characterization of the mandibular shape with 3D landmarks, along with higher density genotyping, yields better insights into the genetic architecture of mandibular development. Most of the main variation is, nonetheless, preferentially embedded in the natural 2D plane of the hemi-mandible, reinforcing the results of earlier influential investigations.

Kinetics genetics: Incorporating the concept of genomic balance into an understanding of quantitative traits

While most mutations are recessive, variants that affect quantitative traits are largely semi-dominant in their action making hybrids between divergent genotypes intermediate. In parallel, changes in chromosomal dosage (aneuploidy) for multiple regions of the genome modulate quantitative characters. We have previously argued that these observations are a reflection of a common process, originating from the more or less subtle effects of changes in dosage on the action of multi-subunit regulatory machineries. Kinetic analyses that vary the amount of one subunit of a complex while holding others constant do not always predict a linear response for the production of the whole. Indeed, in many instances, strong non-linear effects are expected. Here, we advocate that these kinetic observations and predictions should be incorporated into quantitative genetics thought.

Common mechanisms in development and disease: BMP signaling in craniofacial development

BMP signaling is one of the key pathways regulating craniofacial development. It is involved in the early patterning of the head, the development of cranial neural crest cells, and facial patterning. It regulates development of its mineralized structures, such as cranial bones, maxilla, mandible, palate, and teeth. Targeted mutations in the mouse have been instrumental to delineate the functional involvement of this signaling network in different aspects of craniofacial development. Gene polymorphisms and mutations in BMP pathway genes have been associated with various non-syndromic and syndromic human craniofacial malformations. The identification of intricate cellular interactions and underlying molecular pathways illustrate the importance of local fine-regulation of Bmp signaling to control proliferation, apoptosis, epithelial-mesenchymal interactions, and stem/progenitor differentiation during craniofacial development. Thus, BMP signaling contributes both to shape and functionality of our facial features. BMP signaling also regulates postnatal craniofacial growth and is associated with dental structures life-long. A more detailed understanding of BMP function in growth, homeostasis, and repair of postnatal craniofacial tissues will contribute to our ability to rationally manipulate this signaling network in the context of tissue engineering.

Mapping of Craniofacial Traits in Outbred Mice Identifies Major Developmental Genes Involved in Shape Determination

The vertebrate cranium is a prime example of the high evolvability of complex traits. While evidence of genes and developmental pathways underlying craniofacial shape determination is accumulating, we are still far from understanding how such variation at the genetic level is translated into craniofacial shape variation. Here we used 3D geometric morphometrics to map genes involved in shape determination in a population of outbred mice (Carworth Farms White, or CFW). We defined shape traits via principal component analysis of 3D skull and mandible measurements. We mapped genetic loci associated with shape traits at ~80,000 candidate single nucleotide polymorphisms in ~700 male mice. We found that craniofacial shape and size are highly heritable, polygenic traits. Despite the polygenic nature of the traits, we identified 17 loci that explain variation in skull shape, and 8 loci associated with variation in mandible shape. Together, the associated variants account for 11.4% of skull and 4.4% of mandible shape variation, however, the total additive genetic variance associated with phenotypic variation was estimated in ~45%. Candidate genes within the associated loci have known roles in craniofacial development; this includes 6 transcription factors and several regulators of bone developmental pathways. One gene, Mn1, has an unusually large effect on shape variation in our study. A knockout of this gene was previously shown to affect negatively the development of membranous bones of the cranial skeleton, and evolutionary analysis shows that the gene has arisen at the base of the bony vertebrates (Eutelostomi), where the ossified head first appeared. Therefore, Mn1 emerges as a key gene for both skull formation and within-population shape variation. Our study shows that it is possible to identify important developmental genes through genome-wide mapping of high-dimensional shape features in an outbred population.

Formation of the face, mandible, and skull is determined in part by genetic factors, but the relationship between genetic variation and craniofacial development is not well understood. We demonstrate how recent advances in mouse genomics and statistical methods can be used to identify genes involved in craniofacial development. We use outbred mice together with a dense panel of genetic markers to identify genetic loci affecting craniofacial shape. Some of the loci we identify are also known from past studies to contribute to craniofacial development and bone formation. For example, the top candidate gene identified in this study, Mn1, is a gene that appeared at a time when animals started to form bony skulls, suggesting that it may be a key gene in this evolutionary innovation. This further suggests that Mn1 and other genes involved in head formation are also responsible for more fine-grained regulation of its shape. Our results confirm that the outbred mouse population used in this study is suitable to identify single genetic factors even under conditions where many genes cooperate to generate a complex phenotype.

Regulation of Jaw Length During Development, Disease, and Evolution

Molecular and cellular mechanisms that control jaw length are becoming better understood. This is significant since the jaws are not only critical for species-specific adaptation and survival, but they are often affected by a variety of size-related anomalies including mandibular hypoplasia, retrognathia, asymmetry, and clefting. This chapter overviews how jaw length is established during the allocation, proliferation, differentiation, and growth of jaw precursor cells, which originate from neural crest mesenchyme (NCM). The focus is mainly on results from experiments transplanting NCM between quail and duck embryos. Quail have short jaws whereas those of duck are relatively long. Quail-duck chimeras reveal that the determinants of jaw length are NCM mediated throughout development and include species-specific differences in jaw progenitor number, differential regulation of various signaling pathways, and the autonomous activation of programs for skeletal matrix deposition and resorption. Such insights help make the goal of devising new therapies for birth defects, diseases, and injuries to the jaw skeleton seem ever more likely.

Toward an orofacial gene regulatory network

Orofacial clefting is a common birth defect with significant morbidity. A panoply of candidate genes have been discovered through synergy of animal models and human genetics. Among these, variants in interferon regulatory factor 6 (IRF6) cause syndromic orofacial clefting and contribute risk toward isolated cleft lip and palate (1/700 live births). Rare variants in IRF6 can lead to Van der Woude syndrome (1/35,000 live births) and popliteal pterygium syndrome (1/300,000 live births). Furthermore, IRF6 regulates GRHL3 and rare variants in this downstream target can also lead to Van der Woude syndrome. In addition, a common variant (rs642961) in the IRF6 locus is found in 30% of the world's population and contributes risk for isolated orofacial clefting. Biochemical studies revealed that rs642961 abrogates one of four AP-2alpha binding sites. Like IRF6 and GRHL3, rare variants in TFAP2A can also lead to syndromic orofacial clefting with lip pits (branchio-oculo-facial syndrome). The literature suggests that AP-2alpha, IRF6 and GRHL3 are part of a pathway that is essential for lip and palate development. In addition to updating the pathways, players and pursuits, this review will highlight some of the current questions in the study of orofacial clefting.

Gene dosage imbalances: action, reaction, and models

Single-gene deletions, duplications, and misregulation, as well as aneuploidy, can lead to stoichiometric imbalances within macromolecular complexes and cellular networks, causing their malfunction. Such alterations can be responsible for inherited or somatic genetic disorders including Mendelian diseases, aneuploid syndromes, and cancer. We review the effects of gene dosage alterations at the transcriptomic and proteomic levels, and the various responses of the cell to counteract their effects. Furthermore, we explore several biochemical models and ideas that can provide the rationale for treatments modulating the effects of gene dosage imbalances.

Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.

X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses

X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females (XX). Ohno proposed that to achieve a proper balance between X-linked and autosomal genes, those on the active X should also undergo a 2-fold upregulation. Although some support for Ohno's hypothesis has been provided through the years, recent genomic studies testing this hypothesis have brought contradictory results and fueled debate. Thus far, there are as many results in favor as against Ohno's hypothesis, depending on the nature of the datasets and the various assumptions and thresholds involved in the analyses. However, they have confirmed the importance of dosage balance between X-linked and autosomal genes involved in stoichiometric relationships. These facts as well as questions and hypotheses are discussed below.

Use of a natural hybrid zone for genomewide association mapping of craniofacial traits in the house mouse

The identification of the genes involved in morphological variation in nature is still a major challenge. Here, we explore a new approach: we combine 178 samples from a natural hybrid zone between two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus), and high coverage of the genome (~ 145K SNPs) to identify loci underlying craniofacial shape variation. Due to the long history of recombination in the hybrid zone, high mapping resolution is anticipated. The combination of genomes from subspecies allows the mapping of both, variation within subspecies and inter-subspecific differences, thereby increasing the overall amount of causal genetic variation that can be detected. Skull and mandible shape were measured using 3D landmarks and geometric morphometrics. Using principal component axes as phenotypes, and a linear mixed model accounting for genetic relatedness in the mapping populations, we identified nine genomic regions associated with skull shape and 10 with mandible shape. High mapping resolution (median size of significant regions = 148 kb) enabled identification of single or few candidate genes in most cases. Some of the genes act as regulators or modifiers of signalling pathways relevant for morphological development and bone formation, including several with known craniofacial phenotypes in mice and humans. The significant associations combined explain 13% and 7% of the skull and mandible shape variation, respectively. In addition, a positive correlation was found between chromosomal length and proportion of variation explained. Our results suggest a complex genetic architecture for shape traits and support a polygenic model.

Msx1 role in craniofacial bone morphogenesis

The homeobox gene Msx1 encodes a transcription factor that is highly expressed during embryogenesis and postnatal development in bone. Mutations of the MSX1 gene in humans are associated with cleft palate and (or) tooth agenesis. A similar phenotype is observed in newborn mice invalidated for the Msx1 gene. However, little is known about Msx1 function in osteoblast differentiation and bone mineralization in vivo. In the present study, we aimed to explore the variations of individualized bone shape in a subtle way avoiding the often severe consequences associated with gene mutations. We established transgenic mice that specifically express Msx1 in mineral-matrix-secreting cells under the control of the mouse 2.3kb collagen 1 alpha 1 (Col1α1) promoter, which enabled us to investigate Msx1 function in bone in vivo. Adult transgenic mice (Msx1-Tg) presented altered skull shape and mineralization resulting from increased Msx1 expression during bone development. Serial section analysis of the mandibles showed a high amount of bone matrix in these mice. In addition, osteoblast number, cell proliferation and apoptosis were higher in Msx1-Tg mice than in controls with regional differences that could account for alterations of bone shape. However, Von Kossa staining and μCT analysis showed that bone mineralization was lower in Msx1-Tg mice than in controls due to alteration of osteoblastic differentiation. Msx1 appears to act as a modeling factor for membranous bone; it stimulates trabecular bone metabolism but limits cortical bone growth by promoting apoptosis, and concomitantly controls the collagen-based mineralization process.

The effects of varying chromosome arm dosage on maize plant morphogenesis

Maize is an especially well-suited species for studying the effects of aneuploidy on plant development. We used B-A translocations and testers that were crossed seven times into inbred W22 to generate a dosage series for 14 chromosome arms. This is the first report of dosage effects on maize morphogenesis using inbred B-A stocks and inbred tester stocks. We compared plants containing one dose or three doses of each of the 14 chromosome arms with plants containing two doses for seven measured traits. These were leaf width, leaf length, plant height, ear height, internode length, ear node circumference, and tassel branch number. We observed the typical maize aneuploid syndrome wherein one dose was more widespread and more severe in its effects than three doses. All but two of the one-dose effects were negative, and all of the three-dose effects were negative. The occurrence of positive responses by hyperploid plants in our earlier B-A-A study and the absence of any positive responses among the hyperploids reported for the 14 simple B-A translocations tested for dosage effects in the present study and previously may reflect gene dosage interaction between the two chromosome arm segments present in the B-A-A translocations. The overall congruence of our results with those of previous studies suggests that the traits measured are quantitative traits controlled by multiple genes whose activities provide a balanced regulation that transcends individual inbred lines or diverse genetic backgrounds and that such genes may be especially abundant in chromosome arm 1L.

Directed Bmp4 expression in neural crest cells generates a genetic model for the rare human bony syngnathia birth defect

Congenital bony syngnathia, a rare but severe human birth defect, is characterized by bony fusion of the mandible to the maxilla. However, the genetic mechanisms underlying this birth defect are poorly understood, largely due to limitation of available animal models. Here we present evidence that transgenic expression of Bmp4 in neural crest cells causes a series of craniofacial malformations in mice, including a bony fusion between the maxilla and hypoplastic mandible, resembling the bony syngnathia syndrome in humans. In addition, the anterior portion of the palatal shelves emerged from the mandibular arch instead of the maxilla in the mutants. Gene expression assays showed an altered expression of several facial patterning genes, including Hand2, Dlx2, Msx1, Barx1, Foxc2 and Fgf8, in the maxillary and mandibular processes of the mutants, indicating mis-patterned cranial neural crest (CNC) derived cells in the facial region. However, despite of formation of cleft palate and ectopic cartilage, forced expression of a constitutively active form of BMP receptor-Ia (caBmprIa) in CNC lineage did not produce the syngnathia phenotype, suggesting a non-cell autonomous effect of the augmented BMP4 signaling. Our studies demonstrate that aberrant BMP4-mediated signaling in CNC cells leads to mis-patterned facial skeleton and congenital bony syngnathia, and suggest an implication of mutations in BMP signaling pathway in human bony syngnathia.

Morphometric growth relationships of the immature human mandible and tongue

The masticatory apparatus is a highly adaptive musculoskeletal complex comprising several relatively independent structural components, which assist in functions including feeding and breathing. We hypothesized that the tongue is elemental in the maintenance of normal ontogeny of the mandible and in its post-natal growth and development, and tested this using a morphometric approach. We assessed tongue and mandibular measurements in 174 (97 male) human cadavers. Landmark lingual and mandibular data were gathered individuals aged between 20 gestational weeks and 3 yr postnatal. In this analysis, geometric morphometrics assisted in visualizing the morphometrical growth changes in the mandible and tongue. A linear correlation in conjunction with principal component analysis further visualized the growth relationship between these structures. We found that the growth of the tongue and mandible were intrinsically linked in size and shape between 20 gestational weeks and 24 months postnatal. However, the mandible continued to change in shape and size into the 3rd yr of life, whereas the tongue only increased in size over this same period of time. These findings provide valuable insights into the allometric growth relationship between these structures, potentially assisting the clinician in predicting the behaviour of these structures in the assessment of malocclusions.

Correlation of 2D:4D digit ratio and craniofacial shape in prepubertal children

OBJECTIVES

The 2D:4D ratio is sexually dimorphic and is considered a proxy of prenatal androgen levels, or, according to recent evidence, is related to genes involved in ocular and palate development. Our aim was to investigate correlation between the 2D:4D ratio and the shape of the craniofacial skeleton in a population of prepubertal children.

METHODS

We conducted a cross-sectional study in a group of 58 male and 59 female prepubertal children aged 7-12 years. Craniofacial shape was evaluated using 15 skeletal landmarks on lateral cephalometric radiographs and fingers were measured with a computer-assisted procedure that involved tracing the finger outline. Geometric morphometric analysis was applied to the craniofacial landmarks and multivariate regression between digit ratios and craniofacial shape was computed in shape space and form space.

RESULTS

The male 2D:4D ratio was smaller than the female ratio (Cohen's d: 0.275 left hand, 0.126 right hand), but the difference was not statistically significant. Craniofacial shape did not show sexual dimorphism, but males were larger than females. No correlation was found between digit ratio and craniofacial shape in prepubertal children, either for the whole sample or for any of the two sex groups.

CONCLUSIONS

As several factors might be involved in the development and growth of both the craniofacial complex and fingers, the 2D:4D ratio, a putative proxy for fetal sex-hormone levels, is probably unable to impose a measurable effect within the variation of a normal population. Future research needs to examine an adult sample for potential covariation arising after the pubertal growth spurt.

Haploinsufficiency of interferon regulatory factor 6 alters brain morphology in the mouse

Orofacial clefts are among the commonest birth defects. Among many genetic contributors to orofacial clefting, Interferon Regulatory Factor 6 (IRF6) is unique since mutations in this gene cause Van der Woude (VWS), the most common clefting syndrome. Furthermore, variants in IRF6 contribute to increased risk for non-syndromic cleft lip and/or palate (NSCL/P). Our previous work shows that individuals with either VWS or NSCL/P may have cerebral anomalies (larger anterior, smaller posterior regions), and a smaller cerebellum. The objective of this study was to test the hypothesis that disrupting Irf6 in the mouse will result in quantitative brain changes similar to those reported for humans with VWS and NSCL/P. Male mice heterozygous for Irf6 (Irf6(gt1/+); n = 9) and wild-type (Irf6(+/+) ; n = 6) mice at comparable age underwent a 4.7-T MRI scan to obtain quantitative measures of cortical and subcortical brain structures. There was no difference in total brain volume between groups. However, the frontal cortex was enlarged in the Irf6(gt1/+) mice compared to that of wild types (P = 0.028) while the posterior cortex did not differ. In addition, the volume of the cerebellum of Irf6(gt1/+) mice was decreased (P = 0.004). Mice that were heterozygous for Irf6 showed a similar pattern of brain anomalies previously reported in humans with VWS and NSCL/P. These structural differences were present in the absence of overt oral clefts. These results support a role for IRF6 in brain morphometry and provide evidence for a potential genetic link to abnormal brain development in orofacial clefting.