Cloning and transcriptional analysis of the segmentation gene fushi tarazu of Drosophila

In the course of studying the Antennapedia (Antp) locus, we found that one of the 3' Antp exons has weak cross-homology to another gene affecting segmentation, fushi tarazu (ftz; meaning "not enough segments"), which is 30 kb to the left of Antp. Homozygous ftz- embryos die before hatching and lack alternate body segments. The reduced number of segments results from the fusion of the anterior portion of one segment with the posterior portion of the next segment. The ftz gene encodes a single 1.9 kb poly(A)+ RNA expressed exclusively from the early blastoderm to gastrula stages of embryonic development. The structure of the ftz gene has been analyzed by S1 nuclease mapping and by restriction mapping of a cDNA clone. The ftz gene consists of two exons, and it is the 3' exon that cross-hybridizes with the 3' exon of Antp. The role of ftz in cell determination is discussed.     

Mouse Hox-2.2 specifies thoracic segmental identity in Drosophila embryos and larvae

The mouse genome has a number of homeobox genes that are structurally similar to the Drosophila Antenapedia (Antp) gene. We find that one of the mouse Antp-like genes, Hox-2.2, when expressed in developing Drosophila cells under control of a heat shock promoter, can induce homeotic transformations that are nearly identical to those caused by ectopic expression of Antp. In larvae, the Hox-2.2-induced transformations include thoracic denticle belts in place of head structures; in adults, the Hox-2.2 transformations include thoracic legs in place of antennae. The phenotypic effects of Hox-2.2 do not depend on the endogenous Antp gene, whose spatial limits of expression are unaffected by Hox-2.2 expression. Thus, in the Drosophila embryo, Hox-2.2 can substitute for some of the segmental identity functions of Antp, presumably by regulating the same set of downstream genes.     

Ectopic Expression of the Drosophila Homeotic Gene Proboscipedia under Antennapedia P1 Control Causes Dominant Thoracic Defects

A deletion mutation in the Antennapedia Complex of Drosophila melanogaster, Df(3R)SCBXL2, induces both dominant and recessive loss-of-function phenotypes. The deletion is associated with diminished function of proboscipedia (pb), a homeotic gene required for mouthparts formation. Df(3R)SCBXL2 also has associated dominant thoracic defects related to diminished expression of the homeotic Antennapedia (Antp) gene copy on the homologous chromosome. This is shown to be a consequence of ectopic pb expression in the thorax. Newly juxtaposed Antp sequences provide the pb gene on the deletion bearing chromosome with a second promoter, Antp P1, in addition to its own. Ectopic pb protein expression occurs under Antp P1 control, by alternate splicing, and results in diminished accumulation of Antp protein in the imaginal disc cells where Antp P1 is normally expressed. The analysis of this mutant chromosome thus demonstrates that pb protein is capable of participating in the negative regulation of a more posteriorly expressed homeotic gene, as well as serving a homeotic "selector" function in the head.     

The localization and regulation of Antennapedia protein expression in Drosophila embryos

The homeotic Antennapedia (Antp) gene of Drosophila is required for the normal differentiation of the thoracic segments during embryonic development and metamorphosis. Antibodies to a recombinant Antp protein were used to localize the protein in whole mount embryos. Antp is expressed in the nuclei of cells of the thoracic embryonic epidermis and several segments of the ventral and peripheral nervous systems. Analysis of Antp expression in mutant embryos revealed three levels of Antp regulation by genes of the bithorax complex, pleiotropic homeotic loci, and Antp itself. The distributions of the Antp and the Ultrabithorax (Ubx) proteins in doubly-labeled embryos suggest that the Ubx protein may be one direct negative regulator of Antp gene expression.     

Misregulation of homeotic gene expression in Drosophila larvae resulting from mutations at the extra sex combs locus

Using monoclonal antibodies specific for their protein products, the expression of the Ubx, Antp, and Scr genes was examined in imaginal discs and central nervous systems of esc-Drosophila larvae. In esc-mutants, both the Ubx and Scr proteins are expressed at increased levels or in new locations in the leg discs. Ubx also is expressed in new locations in the posterior wing disc and in small groups of cells in the antenna disc. The Antp protein is expressed ectopically in the eye-antenna disc; however, obvious abnormal expression of Antp was not found in the thoracic imaginal discs. Particularly striking is the fact that a single disc, such as the mesothoracic leg, can show increased expression of both a more "anterior" homeotic gene (Scr) and a more "posterior" gene (Ubx). Ectopic expression of Ubx and Antp, but not of Scr, is seen in the central nervous system of mutant larvae. These results are discussed with respect to the adult esc-phenotype and the differential effects of esc mutations on early and late development.     

Homeoboxes in cnidarians.

Homeoboxes have previously been documented from various phyla of triploblastic, coelomate and pseudocoelomate, animals. We report here the first homeoboxes from cnidarians, a phylum of diploblastic organisms thought to occupy a near-basal position in metazoan phylogeny. We have sequenced three partial (77 bp) fragments of Antennapedia (Antp) class homeoboxes from the hydroids Hydractinia symbiolongicarpus and Eleutheria dichotoma. A pair of fragments, Cnox-2-Hs and Cnox-2-Ed, from the two species differ in nucleotide sequences but have identical derived amino acid sequences. A gene tree produced by parsimony analysis shows that these two fragments cluster within the Antp homeobox lineage. The third fragment, Cnox-1, clusters as a sister group of the other Antp class homeoboxes.     

Machine learning based CRISPR gRNA design for therapeutic exon skipping

Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments that require frequent dosing. CRISPR-Cas9 based genome editing that causes exon skipping is a promising therapeutic modality that may offer permanent alleviation of genetic disease. We show that machine learning can select Cas9 guide RNAs that disrupt splice acceptors and cause the skipping of targeted exons. We experimentally measured the exon skipping frequencies of a diverse genome-integrated library of 791 splice sequences targeted by 1,063 guide RNAs in mouse embryonic stem cells. We found that our method, SkipGuide, is able to identify effective guide RNAs with a precision of 0.68 (50% threshold predicted exon skipping frequency) and 0.93 (70% threshold predicted exon skipping frequency). We anticipate that SkipGuide will be useful for selecting guide RNA candidates for evaluation of CRISPR-Cas9-mediated exon skipping therapy.     

The Relationship between the Functional Complexity and the Molecular Organization of the ANTENNAPEDIA Locus of DROSOPHILA MELANOGASTER

The Antp locus is involved in the development of the thorax of the larval and adult Drosophila. The absence of Antp+ function during embryogenesis results in the larval mesothorax exhibiting characteristics of the prothorax and an ensuing lethality; the loss of Antp+ function in the development of the adult thorax causes specific portions of the leg, wing and humeral imaginal discs to develop abnormally. Every Antp mutation, however, does not cause all of these developmental defects. Certain mutant alleles disrupt humeral and wing disc development without affecting leg development, and they are not deficient for the wild-type function required during embryogenesis. Other Antp mutations result in abnormal legs, but do not alter dorsal thoracic development. Mutations of each type can complement to produce a normal adult fly, which suggests that there are at least two discrete functional units within the locus. This hypothesis is supported by the fact that each of the developmental defects arises from the alteration of a different physical region within the Antp DNA. These observations indicate that the complete developmental role of the Antp locus is defined by the spatial and temporal regulation of the expression of several individual functional units.