Genetic Analysis of the Antennapedia Gene Complex (Ant-C) and Adjacent Chromosomal Regions of DROSOPHILA MELANOGASTER. II. Polytene Chromosome Segments 84A-84B1,2

The existence of a gene complex in the proximal right arm of chromosome 3 of Drosophila melanogaster involved in the development of the head and thorax was originally suggested by the phenotypes of several dominant homoeotic mutations and their revertants. A screen for mutations utilizing Df(3R) Antp^Ns+R17 (proximally broken in salivary region 84B1,2) yielded, among 102 recovered mutations, 17 localized by deficiency mapping to the putative homoeotic cluster. These fell into four complementation groups, two of which were characterized by homoeotic phenotypes. To explore the limits of the Antennapedia gene complex (ANT-C) more proximally, a second screen has been undertaken utilizing Df(3R)Scr, a deficiency of 84A1–B1,2.—Of 2832 chromosomes screened, 21 bearing alterations localized to polytene interval 84A–84B1,2 have been recovered. Sixteen are recessive lethals, and five showing reduced viability display a visible phenotype in surviving individuals. Complementation and phenotypic analyses revealed four complementation groups proximal to those identified in the previous screen, including two new alleles of the recessive homoeotic mutation, proboscipedia (pb). Ten of the new mutations correspond to complementation groups defined previously in the Df(3R)Antp^Ns+R17 screen four to the EbR11 group, two to the Scr group and four to the Antp group.—On the basis of the phenotypes of the 39 mutations localized to this region, plus their interactions with extant homoeotic mutations, we postulate that there are at least five functional sites comprising the ANT-C. Three have been demonstrated to be homoeotic in nature. The specific homoeotic transformations thus far observed suggest that these loci are critical for normal development of adult labial, maxillary and thoracic structures.     

Analysis of larval segmentation in lethal genotypes associated with the antennapedia gene complex in Drosophila melanogaster

The segment pattern of larval cuticular structures was examined for individuals bearing lethal genotypes associated with the Antennapedia gene complex (ANT-C). The results provide new evidence for the role of this complex in body segmentation in Drosophila and demonstrate that the ANT-C, like the bithorax complex, effects both larval and imaginal tissues. Lethal genotypes involving new EMS induced lesions or dominant homoeotic mutations (Antp or Antp^Scx) of the Antennapedia complementation group show anomalies in the larval meso- and metathorax. The phenotype is interpreted as a homoeotic transformation of the meso- and metathorax to prothorax. We suggest that Antp⁺ functions in the elicitation of mesothoracic development above that of a prothoracic level in the ventral meso- and metathorax. The lethality of the Sex combs reduced complementation group, which includes the mutation Multiple sex combs (Msc), is characterized by incomplete head formation and the lack of definitive prothoracic ventral setal belts. These results indicate that Scr⁺ is necessary for normal development of the prothorax and are consistent with earlier interpretations based on adult phenotypes. Five other lethal complementation sites, assigned to polytene chromosome interval 84A-B1,2 have been analyzed. They are not associated with dominant homoeotic phenotypes in the adult. The terminal phenotype of individuals carrying lethal mutations in the W36, R11, or R14 complementation groups demonstrate that these loci are important in normal anterior development and/or body segmentation and suggest functional relationships to the homoeotic mutations previously localized to the 84A-84B1,2 polytene interval.     

A genome-wide linkage scan in Tunisian families identifies a novel locus for non-syndromic posterior microphthalmia to chromosome 2q37.1

Posterior microphthalmia (PM) is a relatively rare autosomal recessive condition with normal anterior segment and small posterior segment resulting in high hyperopia and retinal folding. It is an uncommon subtype of microphthalmia that has been mostly reported to coexist with several other ophthalmic conditions and to occur in sporadic cases. The membrane-type frizzled-related protein (MFRP) is the only gene so far reported implicated in autosomal recessive, non-syndromic and syndromic forms of PM. Here, we performed a clinical and genetic analysis using six consanguineous families ascertained from different regions of Tunisia and affected with non-syndromic PM that segregates as an autosomal recessive trait. To identify the disease-causing defect in these families, we first analysed MFRP gene, then some candidate genes (CHX10, OPA1, MITF, SOX2, CRYBB1-3 and CRYBA4) and loci (MCOP1, NNO1 and NNO2) previously implicated in different forms of microphthalmia. After exclusion of these genes and loci, we performed a genome-wide scan using a high density single nucleotide polymorphism (SNP) array 50 K in a large consanguineous pedigree. SNP genotyping revealed eight homozygous candidate regions on chromosomes 1, 2, 3, 6, 15, 17 and 21. Linkage analysis with additional microsatellite markers only retained the 2q37.1 region with a maximum LOD score of 8.85 obtained for D2S2344 at θ = 0.00. Further investigations are compatible for linkage of four more families to this region with a refined critical interval of 2.35 Mb. The screening of five candidate genes SAG, PDE6D, CHRND, CHRNG and IRK13 did not reveal any disease-causing mutation.     

Brista: a gene involved in the specification and differentiation of distal cephalic and thoracic structures in Drosophila melanogaster

Summary A gene Brista has been identified in chromosome 2R, in the region 60D11-E4, in which mutations cause homoeotic transformation of distal antennal structures to distal leg derivatives, and in which certain alleles also lead to upsets in the formation of distal elements of the legs. This gene is haploinsufficient for the homoeotic phenotype. Several putative null and two hypomorphic alleles have been recovered. The effects of exposure to the non-permissive temperature of a temperature-sensitive allele are cummulative and depend upon the length of the exposure during the period of antennal cell proliferation. It is suggested that this gene contributes to the stability of the state of determination in distal domain of the antennal and leg discs, and its relationship to other genes with similar mutant phenotype is discussed.     

Restriction-map variation at the zeste-tko region in natural populations of Drosophila melanogaster

Restriction-map variation in 64 X chromosome lines extracted from three different natural populations of Drosophila melanogaster was investigated with seven six-nucleotide-recognizing enzymes for a 20-kb region including the zeste and tko genes. Ten restriction-site and four length polymorphisms (two insertions and two deletions) were detected. Contrary to the predicted lower level of variation for genes on the X chromosome, the level of variation attributable to nucleotide substitution (estimated heterozygosity/nucleotide = 0.004) was similar to that previously reported for autosomal loci. The amount of insertion/deletion variation in the studied region was within the range observed in autosomal regions and thus not explainable by a simple selection model against the effects of insertional mutations. A general lack of linkage disequilibrium between polymorphic sites was observed.      

Clinical and molecular analysis of the enamelin gene ENAM in Colombian families with autosomal dominant amelogenesis imperfecta

In this study, we analyzed the phenotype, clinical characteristics and presence of mutations in the enamelin gene ENAM in five Colombian families with autosomal dominant amelogenesis imperfecta (ADAI). 22 individuals (15 affected and seven unaffected) belonging to five Colombian families with ADAI and eight individuals (three affected and five unaffected) belonging to three Colombian families with autosomal recessive amelogenesis imperfecta (ARAI) that served as controls for molecular alterations and inheritance patterns were studied. Clinical, radiographic and genetic evaluations were done in all individuals. Eight exons and three intron-exon boundaries were sequenced for mutation analysis. Two of the five families with ADAI had the hypoplasic phenotype, two had the hypocalcified phenotype and one had the hypomaturative phenotype. Anterior open bite and mandibular retrognathism were the most frequent skeletal abnormalities in the families with ADAI. No mutations were found. These findings suggest that ADAI in these Colombian families was unrelated to previously described mutations in the ENAM gene. These results also indicate that other regions not included in this investigation, such as the promoter region, introns and other genes should be considered as potential ADAI candidates.     

Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such putative mutations was larger than has been previously reported; this yield was in part due to the comprehensive and uniform coverage afforded by WGS. Deleterious variants were found in four unrecognized, nine known, and eight candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to FMR1, which is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.     

Mutants of the bithorax complex and determinative states in the thorax of Drosophila melanogaster.

Homoeotic mutations of the bithorax complex cause segmental transformations. The genes in which these mutations occur are good candidates for genes that are involved in determination. The determination system in imaginal discs must have at least two functions. One is a cell heredity function that is responsible for maintaining the determined state during growth and development. A second is the expression of the determined state (e.g., different imaginal discs have different morphologies). The homoeotic mutations of the bithorax complex could be affecting either of these two functions. I have found that when posterior haltere disc cells, that are transformed by the mutation postbithorax so that they form wing cuticle in situ, regenerate anterior structures, these structures are anterior wing. This is the same result as that seen when wild-type posterior-wing disc cells regenerate anterior structures. On the other hand, when anterior haltere disc cells transformed by the mutation bithorax³, so that they produce wing cuticle in situ, regenerate, they produce posterior haltere structures. This is unlike wild-type anterior-wing disc cells, which regenerate posterior-wing structures. From these results, I conclude that bithorax³ affects the expression of the determined state and postbithorax affects the cell heredity of determination.     

A genetic screen for elements of the network that regulates neurogenesis in Drosophila

The development of external sensory organs on the notum of Drosophila is promoted by the proneural genes achaete and scute. Their activity defines proneural cell clusters in the wing imaginal disc. Ectopic expression, under control of the GAL4 system, of the proneural gene lethal of scute (l'sc) causes the development of ectopic bristles. Persistent ectopic expression of l'sc is not sufficient to impose a neural fate on any given cell. This implies that mutual inhibition, mediated by the Notch signaling pathway, occurs among the cells of the ectopic proneural cluster. Consequently, the dominant, quantifiable phenotype associated with ectopic expression of l'sc is modified by mutations in genes known to be involved in neurogenesis. This phenotype has been utilized to screen for dominant enhancers and suppressors that modify the number of ectopic bristles. In this way, about 100 000 progeny of EMS or X-ray-treated flies have been analyzed to identify autosomal genes involved in regulation of the neural fate. In addition 1200 chromosomes carrying lethal P-element insertions were screened for modifiers. Besides mutations in genes expected to modify the phenotype, we have isolated mutations in six genes not known so far to be involved in neurogenesis.     

A developmental genetic analysis of the gene Regulator of postbithorax in Drosophila melanogaster

We report the characterization of loss-of-function alleles of the homoeotic mutation Regulator of postbithorax (Rg-pbx) in Drosophila melanogaster. Rg-pbx is a dominant gain-of-function mutation which shows a transformation of posterior haltere to wing in the adult cuticle. This mutant phenotype mimics that of the bithorax complex lesion postbithorax (pbx). Loss-of-function alleles described here are lethal in the embryonic stage and affect the pattern of segmentation of the embryo. Examination of the terminal phenotype of null and hypomorphic alleles of Rg-pbx has shown that inactivation of the Rg-pbx gene leads to loss of the thoracic segments and the adjacent labial segment of the Drosophila embryo. An effect of the mutations is also seen in the seventh and eighth abdominal segments of embryos. The loss-of-function phenotype is similar to that described for the segmentation mutant hunchback (hb). Complementation tests show that Rg-pbx and hb are allelic. Temperature shift experiments using a temperature-sensitive loss-of-function allele show that the Rg-pbx gene product is required early in embryogenesis. We further report that the dominant Rg-pbx phenotype is sensitive to the gene dosage of another segmentation-controlling gene, fushi tarazu (ftz). Flies carrying a mutant copy of the ftz gene in trans to Rg-pbx show a dramatic enhancement of the penetrance of the homoeotic mutant phenotype. We were also able to demonstrate a suppression of the Rg-pbx phenotype by the addition of a duplication for the ftz⁺ gene to an Rg-pbx stock. Examination of the phenotype of ftz⁻, Rg-pbx⁻ double-mutant embryos did not reveal a clear pattern of epistasis between the genes nor was absolute additivity of phenotype seen. A possible formal relationship between Rg-pbx, ftz, and the postbithorax (pbx) locus is proposed.     

Pattern formation and determination in the antenna of the homoeotic mutant Antennapedia of Drosophila melanogaster

The development of the antenna in the antennal-leg homoeotic mutant Antennapedia (Antp^R) was investigated using somatic crossing-over to mark clones of cells in Antp^R antennal appendages. Antp^R antennae ranged from a nearly normal antenna to a nearly normal leg. The arrangement of clones of marked bristles and cuticle in the more antennalike antennae was similar to the wild type antenna, and that of the leglike antennae was similar to the wild-type leg. The contiguity of clones argued against extensive individual cell migration. The regions occupied by homoeotic leg varied considerably between different Antp^R antennae. Observation of Antp^R antennae in these phenotypic mosaics showed that specific leg parts replaced specific antennal parts. Even small groups of leg sensilla appeared only at precise locations in the antenna. These results suggest that homoeotic leg cells and antennal cells can both respond to the same positional information or prepattern. An analysis of clone size provided estimates for cell number in the Antp^R antenna. It was found that cell numbers in the wild-type and Antp^R antennae are about the same until the third instar, when the Antp^R cells start dividing more rapidly than wild type. Previous work had shown that clonal inheritance of a commitment for homoeotic leg also did not occur prior to the early third instar. It is suggested that determination for homoeotic leg occurs in the early third instar, and that thereafter this commitment is inherited by the progeny of the determined cells. The increase in growth rate is probably due to a faster growth rate in cells with a leg commitment than in cells with an antennal commitment. The results suggest that, once initiated, determination may be of two types—a clonally inherited determination (for example, to be homoeotic leg) and an environmental determination (for example, to be a specific part of a homoeotic leg). Clonal inheritance of determination in normal embryonic development and in sex determination in intersexes is discussed.     

Study of dosage compensation in Drosophila

Using a sensitive RT-QPCR assay, we analyzed the regulatory effects of sex and different dosage compensation mutations in Drosophila. To validate the assay, we showed that regulation for several genes indeed varied with the number of functional copies of that gene. We then confirmed that dosage compensation occurred for most genes we examined in male and female flies. Finally, we examined the effects on regulation of several genes in the MSL pathway, presumed to be involved in sex-dependent determination of regulation. Rather than seeing global alterations of either X chromosomal or autosomal genes, regulation of genes on either the X chromosome or the autosomes could be elevated, depressed, or unaltered between sexes in unpredictable ways for the various MSL mutations. Relative dosage for a given gene between the sexes could vary at different developmental times. Autosomal genes often showed deranged regulatory levels, indicating they were in pathways perturbed by X chromosomal changes. As exemplified by the BR-C locus and its dependent Sgs genes, multiple genes in a given pathway could exhibit coordinate regulatory modulation. The variegated pattern shown for expression of both X chromosomal and autosomal loci underscores the complexity of gene expression so that the phenotype of MSL mutations does not reflect only simple perturbations of genes on the X chromosome.     

Homoeosis in Drosophila: a new enhancer of polycomb and related homoeotic mutations

A new recessive lethal mutation in Drosophila melanogaster , Enhancer of Polycomb [E(Pc)], and chromosomal deficiencies lacking this locus act as dominant enhancers of the Polycomb mutant syndrome in adults. Thus, although E(Pc)/+ flies are phenotypically normal, this locus is haplo-abnormal with respect to its effect on the Polycomb phenotype. Recombinational and deficiency mapping localize the E(Pc) locus on chromosome 2 proximally and very closely linked (~0.1 map unit) to the engrailed gene. E(Pc) enhances the expression of all Polycomb point mutations examined including that of a deficiency, indicating that this interaction does not depend on the presence of an altered Polycomb gene product. In several respects the mutations extra sex comb, lethal(4)29, and Polycomblike resemble those at the Polycomb locus. In the presence of E(Pc), recessive alleles of extra sex comb and lethal(4)29 are rendered slightly pseudodominant, and the homoeotic effects of Polycomblike heterozygotes are also enhanced. However, E(Pc) does not affect the expression of dominant mutations within the Bithorax gene complex (Cbx) or Antennapedia gene complex (Antp^Ns, Antp^73b, Antp^scx , Antp^EfW15, Scr^Msc) which give homoeotic transformations resembling those of the Polycomb syndrome. Available evidence from the study of adult phenotypes suggests that mutations at E(Pc) do not result in homoeotic changes directly but instead modify the expression of a specific set of functionally related homoeotic variants.     

Sex Differences in Drosophila melanogaster Heterochromatin Are Regulated by Non-Sex Specific Factors

The eukaryotic genome is assembled into distinct types of chromatin. Gene-rich euchromatin has active chromatin marks, while heterochromatin is gene-poor and enriched for silencing marks. In spite of this, genes native to heterochromatic regions are dependent on their normal environment for full expression. Expression of genes in autosomal heterochromatin is reduced in male flies mutated for the noncoding roX RNAs, but not in females. roX mutations also disrupt silencing of reporter genes in male, but not female, heterochromatin, revealing a sex difference in heterochromatin. We adopted a genetic approach to determine how this difference is regulated, and found no evidence that known X chromosome counting elements, or the sex determination pathway that these control, are involved. This suggested that the sex chromosome karyotype regulates autosomal heterochromatin by a different mechanism. To address this, candidate genes that regulate chromosome organization were examined. In XX flies mutation of Topoisomerase II (Top2), a gene involved in chromatin organization and homolog pairing, made heterochromatic silencing dependent on roX, and thus male-like. Interestingly, Top2 also binds to a large block of pericentromeric satellite repeats (359 bp repeats) that are unique to the X chromosome. Deletion of X heterochromatin also makes autosomal heterochromatin in XX flies dependent on roX and enhances the effect of Top2 mutations, suggesting a combinatorial action. We postulate that Top2 and X heterochromatin in Drosophila comprise a novel karyotype-sensing pathway that determines the sensitivity of autosomal heterochromatin to loss of roX RNA.     

Non-Syndromic Hearing Impairment in India: High Allelic Heterogeneity among Mutations in TMPRSS3, TMC1, USHIC,CDH23 and TMIE

Mutations in the autosomal genes TMPRSS3, TMC1, USHIC, CDH23 and TMIE are known to cause hereditary hearing loss. To study the contribution of these genes to autosomal recessive, non-syndromic hearing loss (ARNSHL) in India, we examined 374 families with the disorder to identify potential mutations. We found four mutations in TMPRSS3, eight in TMC1, ten in USHIC, eight in CDH23 and three in TMIE. Of the 33 potentially pathogenic variants identified in these genes, 23 were new and the remaining have been previously reported. Collectively, mutations in these five genes contribute to about one-tenth of ARNSHL among the families examined. New mutations detected in this study extend the allelic heterogeneity of the genes and provide several additional variants for structure-function correlation studies. These findings have implications for early DNA-based detection of deafness and genetic counseling of affected families in the Indian subcontinent.     

A Genome-Wide Association Study Points out the Causal Implication of SOX9 in the Sex-Reversal Phenotype in XX Pigs

Among farm animals, pigs are known to show XX sex-reversal. In such cases the individuals are genetically female but exhibit a hermaphroditism, or a male phenotype. While the frequency of this congenital disease is quite low (less than 1%), the economic losses are significant for pig breeders. These losses result from sterility, urogenital infections and the carcasses being downgraded because of the risk of boar taint. It has been clearly demonstrated that the SRY gene is not involved in most cases of sex-reversal in pigs, and that autosomal recessive mutations remain to be discovered. A whole-genome scan analysis was performed in the French Large-White population to identify candidate genes: 38 families comprising the two non-affected parents and 1 to 11 sex-reversed full-sib piglets were genotyped with the PorcineSNP60 BeadChip. A Transmission Disequilibrium Test revealed a highly significant candidate region on SSC12 (most significant p-value<4.65.10^-10) containing the SOX9 gene. SOX9, one of the master genes involved in testis differentiation, was sequenced together with one of its main regulatory region Tesco. However, no causal mutations could be identified in either of the two sequenced regions. Further haplotype analyses did not identify a shared homozygous segment between the affected pigs, suggesting either a lack of power due to the SNP properties of the chip, or a second causative locus. Together with information from humans and mice, this study in pigs adds to the field of knowledge, which will lead to characterization of novel molecular mechanisms regulating sexual differentiation and dysregulation in cases of sex reversal.     

Hypomorphic lethal mutations and their implications for the interpretation of lethal complementation studies in Drosophila

In a small region of the X chromosome of Drosophila melanogaster, we have found that a third of the mutations that appear to act as lethals in segmental haploids are viable in homozygous mutant individuals. These viable mutations fall into four complementation groups. The most reasonable explanation of these mutations is that they are a subset of functionally hypomorphic alleles of essential genes: hypomorphic mutations with activity levels above a threshold required for survival, but below twice that level, should behave in this manner. We refer to these mutations as "haplo-specific lethal mutations." In studies of autosomal lethals, haplo-specific lethal mutations can be included in lethal complementation tests without being identified as such. Accidental inclusion of disguised haplo-specific lethals in autosomal complementation tests will generate spurious examples of interallelic complementation.     

Autosomal mutations that interfere with sex determination in somatic cells of Drosophila have no direct effect on the germline

In Drosophila, mutations at the transformer-2, the double-sex, or the intersex loci interfere with the normal sexual development of somatic cells. In order to study the effect of mutations at these loci on germ cell development, mutant germ cells were introduced into normal female or normal male gonads either by pole cell transplantation or by induced mitotic recombination, and their ability to give rise to functional gametes was tested. In contrast to the effects seen in mutant somatic cells, the mutant germ cells ($\text{dsx}\text{dsx}\text{,}\text{dsx}{}^{\mathrm{D}}\text{+}\text{,}\text{dsx}{}^{\mathrm{d}}\text{dsx}\text{,}\text{tra-2}\text{tra-2}\text{,}\text{ix}\text{ix}$) developed normally according to their chromosomal sex, and no sexual transformations of germ cells were observed. In combination with the results of J. L. Marsh and E. Wieschaus (1978, Nature (London)272, 249–251) concerning the transformer locus, it seems that the four autosomal loci known to be involved in sex determination of somatic cells have no important role in the sexual development of the germline. The results are discussed with respect to sex determination in the germline of Drosophila and are compared to observations made on similar mutations in other animal species.