Molecular and cytogenetical characterization of the 10A1-2 band and adjoining region in the Drosophila melanogaster polytene X chromosome

Some 300 kb of DNA from the 9F12-10A7 X chromosome region (seven bands) uncovered by Df(1)vL3 were cloned and 31 break points of chromosome rearrangements within the region were mapped. Positions of 12 genes found earlier in genetic saturation experiments, transcripts and P element-induced mutations were located on the physical map using either chromosome rearrangements or Southern blot hybridizations. Data on the position of the break points, genes and polytene chromosome bands allow the following conclusions to be made. (1) The size of the bands in the region varies between 4 kb (10A6 and 7) and 183-195 kb (10A1-2). The compaction ratio of DNA in bands varies from 8-36 (10A6 + 7) to 151-161 (10A1-2). Therefore, fine and thick bands appear to have different kinds of DNP packaging. (2) The bands differ in genetic content. Fine bands contain from one to three genes. In contrast, the 10A1-2 band contains three genes and at least six transcribed DNA fragments. (3) Comparison of genetic and physical maps shows that in this region 0.01 centiMorgan corresponds to 3.3 kb of DNA.

Microdissected double-minute DNA detects variable patterns of chromosomal localizations and multiple abundantly expressed transcripts in normal and leukemic cells

Double-minute (dm) chromosomes are cytogenetically resolvable DNA amplification-mediating acentric extrachromosomal structures that are commonly seen in primary tumors, tumor cell lines, and drug-resistant cells grown in vitro. Selective isolation of dm DNAs with standard molecular biological techniques is difficult, and thus, detailed studies to elucidate their structure, site of chromosomal origin, and chromosomal reintegration patterns have been limited. In those instances in which a gene has been localized on dms, characterization of the remainder of the DNA, which far exceeds the size of the gene identified, has remained inconclusive, dms seen in the acute myeloid leukemia cell line HL-60 have been shown to harbor the c-myc protooncogene. In this paper, we report the successful isolation of the dm-specific DNAs from these cells by the microdissection/polymerase chain reaction technique and demonstrate that the dm DNAs derived from a single discrete normal chromosome segment 8q24.1-q24.2 reintegrate at various specific locations in the leukemic cells. The microdissected dm DNA detects multiple abundantly expressed transcripts distinct from c-myc mRNA on Northern blots. By devising a "transcript selection" strategy, we cloned the partial genomic sequence of a gene from the microdissected DNA that encodes two of these RNAs. This strategy will be generally applicable for rapid cloning of unknown amplified genes harbored on dms. With DNA from 20 microdissected dms, we constructed a genomic library of about 20,000 recombinant microclones with an average insert size of about 450 bp.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular mechanisms of pattern formation by the BRE enhancer of the Ubx gene

The core activity of the Ubx gene enhancer BRE (bx region enhancer) is encoded within a 500 bp module. bx DNA outside this active module increases the level of expression, expands the expression into ventro-lateral ectoderm and partially stabilizes the late expression pattern. The products of the gap genes hb and tll and of the pair-rule gene ftz bind to the 500 bp BRE module and control directly its initial pattern of expression. ftz enhances expression in even-numbered parasegments within the correct spatial domain whose boundaries are set by hb and tll. In addition, en and twi products activate the enhancer, probably directly. en broadens the parasegmental stripe while twi cooperates with ftz to enhance expression in the mesoderm. Binding sites for the five regulators are closely clustered, often overlapping extensively with one another. In vitro, hb blocks the binding of ftz and can also displace ftz protein pre-bound to an overlapping site, suggesting that competitive binding and/or interference by hb sets the initial boundaries of the domain of expression. Our results also suggest that this interaction is short-range and the long distance interactions among different enhancers may depend on each enhancer's ability to complex with the promoter.

Flow cytometric study of the expression of neutral endopeptidase (CD10/CALLA) on the surface of newborn granulocytes

The susceptibility of newborn infants to bacterial infections is well documented. Neutrophils play an important role in defense against bacterial infection, the most common kind of infection in the newborn period. Many studies of lymphocyte surface characteristics during that period of life are available, but there are no reports on the surface immunophenotype of the granulocytes at birth. Because some of their membrane associated antigens have been identified as enzymes (CALLA/CD10), neutral endopeptidase, and (CD13) amino peptidase that could play a role in the biological functions of neutrophils, a study of the membrane phenotype appeared potentially important. Using flow cytometry, we studied the expression of a panel of the antigens expressed on mature neutrophils including CD10, CD13, and CD33 in 28 full-term babies and 19 adults. A significantly (p < 0.001) lower expression of CD10, CD13, and CD33 was found in full-term babies compared with 19 adults. These data raise two points: first, that because CD10 is detected only on segmented granulocytes, the low level of CD10 observed in neonates is consistent with a degree of immaturity of the neutrophil membrane, and second, that the deficiency of endopeptidase may impair neutrophil interactions with peptide effectors and thus play a role in the increased susceptibility to bacterial infections exhibited in newborns.

Stepwise assembly of hyperaggregated forms of Drosophila zeste mutant protein suppresses white gene expression in vivo

The zeste gene is involved in two chromosome pairing-dependent phenomena: transvection and the suppression of white gene expression. Both require the ability of zeste protein to multimerize, dependent on three interlaced hydrophobic heptad repeats in the C-terminal domain. The first step is dimerization through a leucine zipper. Two other heptad repeats are then required to form higher multimers. The zeta(1) mutation, which causes the pairing-dependent suppression of white, creates a new hydrophobic nucleus that allows the formation of a new and larger aggregate. The zeta(op6) mutation, which suppresses even unpaired copies of white, makes even larger aggregates. The phenotypic suppression of white by a series of mutants is strictly correlated with hyperaggregation and the larger the hyperaggregates, the weaker the requirement for the pairing of white. Hyperaggregation of the Z1 protein in vitro is suppressed by co-translation with the C-terminal peptide of wild-type protein, lacking the DNA-binding domain. This C-Z+ peptide also complements the zeta(1) allele in vivo and restores normal color, demonstrating that zeste product also exists in a multimeric complex in the cell. Complementation in vivo is strictly correlated with the prevention of hyperaggregation of the zeste mutant products in vitro, supporting the interpretation that excessive association of zeta(1) and zeta(op6) proteins is responsible for their repression of white gene expression.

Multimerization of the Drosophila zeste protein is required for efficient DNA binding

The Drosophila zeste protein forms multimeric species in vitro through its C-terminal domain. Multimerization is required for efficient binding to DNA containing multiple recognition sequences and increasing the number of binding sites stimulates binding in a cooperative manner. Mutants that can only form dimers still bind to a dimeric site, but with lower affinity. Mutations or progressive deletions from the C-terminal show that when even dimer formation is prevented, DNA-binding activity is lost. Surprisingly, binding activity is regained with larger deletions that leave only the DNA-binding domain. Additional protein sequences apparently inhibit DNA binding unless they permit multimerization. The DNA-binding domain peptides bind strongly even to isolated recognition sequences and they bind as monomers. The ability of various zeste peptides to stimulate white gene expression in vivo shows that multimeric forms are the functional species of the zeste product in vivo. The DNA-binding domain peptide binds well to DNA in vitro, but it cannot stimulate white gene expression in vivo. This failure may reflect the need for an activation domain or it may be caused by indiscriminate binding of this peptide to non-functional isolated sites. Multimerization increases binding specificity, selecting only sites with multiple recognition sequences.

Related chromosome binding sites for zeste, suppressors of zeste and Polycomb group proteins in Drosophila and their dependence on Enhancer of zeste function

Polycomb group genes are necessary for maintaining homeotic genes repressed in appropriate parts of the body plan. Some of these genes, e.g. Psc, Su(z)2 and E(z), are also modifiers of the zeste-white interaction. The products of Psc and Su(z)2 were immunohistochemically detected at 80-90 sites on polytene chromosomes. The chromosomal binding sites of these two proteins were compared with those of zeste protein and two other Polycomb group proteins, Polycomb and polyhomeotic. The five proteins co-localize at a large number of sites, suggesting that they frequently act together on target genes. In larvae carrying a temperature sensitive mutation in another Polycomb group gene, E(z), the Su(z)2 and Psc products become dissociated from chromatin at non-permissive temperatures from most but not all sites, while the binding of the zeste protein is unaffected. The polytene chromosomes in these mutant larvae acquire a decondensed appearance, frequently losing characteristic constrictions. These results suggest that the binding of at least some Polycomb group proteins requires interactions with other members of the group and, although zeste can bind independently, its repressive effect on white involves the presence of at least some of the Polycomb group proteins.

The su(Hw) protein insulates expression of the Drosophila melanogaster white gene from chromosomal position-effects

Mutations in the suppressor of Hairy-wing [su(Hw)] locus reverse the phenotype of a number of tissue-specific mutations caused by insertion of a gypsy retrotransposon. The su(Hw) gene encodes a zinc finger protein which binds to a 430 bp region of gypsy shown to be both necessary and sufficient for its mutagenic effects. su(Hw) protein causes mutations by inactivation of enhancer elements only when a su(Hw) binding region is located between these regulatory sequences and a promoter. To understand the molecular basis of enhancer inactivation, we tested the effects of su(Hw) protein on expression of the mini-white gene. We find that su(Hw) protein stabilizes mini-white gene expression from chromosomal position-effects in euchromatic locations by inactivating negative and positive regulatory elements present in flanking DNA. Furthermore, the su(Hw) protein partially protects transposon insertions from the negative effects of heterochromatin. To explain our current results, we propose that su(Hw) protein alters the organization of chromatin by creating a new boundary in a pre-existing domain of higher order chromatin structure. This separates enhancers and silencers distal to the su(Hw) binding region into an independent unit of gene activity, thereby causing their inactivation.

Molecular analysis of the zeste-white interaction reveals a promoter-proximal element essential for distant enhancer-promoter communication

We have analyzed the eye and testis enhancers located 1 kb upstream of the transcription start site of the white gene. Both enhancers confer the corresponding tissue-specific expression on a heterologous promoter as well as on the white promoter. The eye determinant consists of multiple elements, each able to stimulate eye-specific expression. It also contains five binding sites for the zeste protein while the immediately adjacent testis element contains none. Site-directed mutation of these zeste binding sites abolishes the zeste-white interaction but does not significantly affect the eye enhancer activity, indicating that they are not important for the eye enhancer activity per se. Other zeste binding sites just upstream of the promoter are not necessary for the zeste-white interaction. We conclude that the overlap of the eye enhancer with the zeste binding sites is responsible for the zeste-white interaction and explains why this interaction affects eye but not testis expression. Sequence deletion or substitution experiments suggested that the white promoter is internal to the transcription start site; the zeste protein is not required for distant enhancer action but a 95-bp promoter-proximal sequence is essential for distant enhancer-promoter interaction. This element may serve as an anchor to stabilize formation of a loop that brings the enhancer to the vicinity of the promoter.

Conserved DNA binding and self-association domains of the Drosophila zeste protein

The zeste gene product is involved in two types of genetic effects dependent on chromosome pairing: transvection and the zeste-white interaction. Comparison of the predicted amino acid sequence with that of the Drosophila virilis gene shows that several blocks of amino acid sequence have been very highly conserved. One of these regions corresponds to the DNA binding domain. Site-directed mutations in this region indicate that a sequence resembling that of the homeodomain DNA recognition helix is essential for DNA binding activity. The integrity of an amphipathic helical region is also essential for binding activity and is likely to be responsible for dimerization of the DNA binding domain. Another very strongly conserved domain of zeste is the C-terminal region, predicted to form a long helical structure with two sets of heptad repeats that constitute two long hydrophobic ridges at opposite ends and on opposite faces of the helix. We show that this domain is responsible for the extensive aggregation properties of zeste that are required for its role in transvection phenomena. A model is proposed according to which the hydrophobic ridges induce the formation of open-ended coiled-coil structures holding together many hundreds of zeste molecules and possibly anchoring these complexes to other nuclear structures.

The giant gene of Drosophila encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes

The sequence of a cDNA from the giant gene of Drosophila shows that its product has a basic domain followed by a leucine zipper motif. Both features contain characteristic conserved elements of the b-ZIP family of DNA-binding proteins. Expression of the gene in bacteria or by in vitro translation yields a protein that migrates considerably faster than the protein extracted from Drosophila embryos. Treatment with phosphatase shows that this difference is due to multiple phosphorylation of the giant protein in the embryo. Ectopic expression of the protein in precellular blastoderm embryos produces abnormal phenotypes with a pattern of segment loss closely resembling that of Kruppel mutant embryos. Immunological staining shows that giant, ectopically expressed from the hsp70 promoter, represses the expression of both the Kruppel and knirps segmentation gap genes. The analysis of the interactions between Kruppel, knirps and giant reveals a network of negative regulation. We show that the apparent positive regulation of knirps by Kruppel is in fact mediated by a negative effect of Kruppel on giant and a negative effect of giant on knirps. giant protein made in bacteria or in embryos binds in vitro to the Kruppel regulatory elements CD1 and CD2 and recognizes a sequence resembling the binding sites of other b-ZIP proteins.

The bx region enhancer, a distant cis-control element of the Drosophila Ubx gene and its regulation by hunchback and other segmentation genes

The Drosophila homeotic gene Ultrabithorax (Ubx) is regulated by complex mechanisms that specify the spatial domain, the timing and the activity of the gene in individual tissues and in individual cells. In early embryonic development, Ubx expression is controlled by segmentation genes turned on earlier in the developmental hierarchy. Correct Ubx expression depends on multiple regulatory sequences located outside the basal promoter. Here we report that a 500 bp DNA fragment from the bx region of the Ubx unit, approximately 30 kb away from the promoter, contains one of the distant regulatory elements (bx region enhancer, BRE). During early embryogenesis, this enhancer element activates the Ubx promoter in parasegments (PS) 6, 8, 10, and 12 and represses it in the anterior half of the embryo. The repressor of the anterior Ubx expression is the gap gene hunchback (hb). We show that the hb protein binds to the BRE element and that such binding is essential for hb repression in vivo, hb protein also binds to DNA fragments from abx and bxd, two other regulatory regions of the Ubx gene. We conclude that hb represses Ubx expression directly by binding to BRE and probably other Ubx regulatory elements. In addition, the BRE pattern requires input from other segmentation genes, among them tailless and fushi tarazu but not Krüppel and knirps.

Interactions of the Drosophila gap gene giant with maternal and zygotic pattern-forming genes

The Drosophila gene giant (gt) is a segmentation gene that affects anterior head structures and abdominal segments A5-A7. Immunolocalization of the gt product shows that it is a nuclear protein whose expression is initially activated in an anterior and a posterior domain. Activation of the anterior domain is dependent on the maternal bicoid gradient while activation of the posterior domain requires maternal nanos gene product. Initial expression is not abolished by mutations in any of the zygotic gap genes. By cellular blastoderm, the initial pattern of expression has evolved into one posterior and three anterior stripes of expression. The evolution, position and width of these stripes are dependent on interactions between gt and the other gap genes. In turn, gt activity in these domains affects the expression of the other gap genes. These interactions, typical of the cross-regulation previously observed among gap genes, confirm that gt is a member of the gap gene class whose function is necessary to establish the overall pattern of gap gene expression. After cellular blastoderm, gt protein continues to be expressed in the head region in parts of the maxillary and mandibular segments as well as in the labrum. Expression is never detected in the labial or thoracic segment primordia but persists in certain head structures, including the ring gland, until the end of embryonic development.

Self-association of the Drosophila zeste protein is responsible for transvection effects

The zeste gene product is required for transvection effects that imply the ability of regulatory elements on one chromosome to affect the expression of the homologous gene in a somatically paired chromosome. The z1 mutation causes a pairing dependent inhibition of the expression of the white gene. Both of these phenomena can be explained by the tendency of zeste protein, expressed in bacteria or in flies, to self-associate, forming complexes of several hundred monomers. These large aggregates bind to DNA and are found in nuclear matrix preparations, probably because they co-sediment with the matrix. The principal determinants of this self-association are located in the C-terminal half of the protein but some limited aggregation is obtained also with the N-terminal half, which contains the DNA binding domain. The z1 and zop2 mutant proteins aggregate to the same degree as the wild type but the z11G3 product, a pseudorevertant of z1, has a reduced tendency to aggregate. This mutation, which in vivo is antagonistic to z1 and does not support transvection effects, can be made to revert its phenotype when the mutant protein is over-produced under the control of the heat shock promoter. These results indicate that both the zeste-white interaction and transvection effects require the formation of high order aggregates. When the z1 protein is over-produced in vivo, it reduces the expression of an unpaired copy of white, indicating that the normal requirement for chromosome pairing is simply a device to increase the size of the aggregate bound to the white regulatory region.

Transvection and long-distance gene regulation

Numerous genes contain regulatory elements located many tens of kilobases away from the promoter they control. Specific mechanisms must be required to ensure that such distant elements can find and interact with their proper targets but not with extraneous genes. This review explores the connections between transvection phenomena, the activation of domains of homeotic gene expression, position effect variegation and silencers. These various examples of long-distance effects suggest that, in all cases, related forms of chromatin packaging may be involved.

The claret locus in Drosophila encodes products required for eyecolor and for meiotic chromosome segregation

The claret (ca) locus in Drosophila encodes products that are needed both for wild-type eyecolor and for correct meiotic chromosome segregation. Mutants described previously provide evidence that two mutationally independent coding regions are present at ca. We have recovered six new P element-induced and one spontaneous ca mutant. Four of these new mutants affect both eyecolor and chromosome segregation. The high frequency of co-mutation of these two functions suggests that the corresponding genes are closely adjacent to one another. We recovered genomic DNA sequences corresponding to the ca locus by chromosome walking, and showed using revertant analysis that the cloned region encodes ca+. Transformation experiments demonstrate that the mutant effect resulting in meiotic chromosome non-disjunction (nd) and loss is fully rescued by DNA from the cloned region. Two RNAs of 7.4 and 2.2 kb have been identified by Northern blot analysis as the putative eyecolor and segregational products. Expression of the RNAs with respect to males and females, and their presence or absence in ca and nd mutants indicate that the 7.4 kb RNA corresponds to the product needed for wild-type eyecolor and the 2.2 kb RNA is the product required for normal chromosome segregation. These RNAs are transcribed in opposite directions to one another. Alleles that affect both eyecolor and chromosome segregation are deletion mutants that affect both transcripts. Thus, the putative eyecolor and segregational products are encoded by separate genes. Mutants that affect both eyecolor and chromosome segregation apparently do so because they delete essential regions of both genes.

A novel spatial transcription pattern associated with the segmentation gene, giant, of Drosophila

The segmentation gene, giant, is located in 3A1 within a cloned chromosome region surrounding the zeste locus. Rearrangement breakpoints associated with giant mutations were localized on the genomic clone map, and nearby transcription units were identified. One transcription unit is active during early embryogenesis and its transcripts are spatially localized from blastoderm into extended germband stages, consistent with expected expression patterns predicted by the 'gap' phenotype of giant mutants. Germ line transformation experiments using a 10-kb DNA fragment containing this transcription unit gave complete rescue of the abdominal giant defect but only partial correction of the head defect. The effect of mutations in three other gap loci, Kr, kni and hb, were also analyzed.

The Drosophila zeste protein binds cooperatively to sites in many gene regulatory regions: implications for transvection and gene regulation

The Drosophila zeste protein binds in vitro to several sites in the white, Ultrabithorax, decapentaplegic, Antennapedia, and engrailed genes and to at least one site in the zeste gene itself. The distribution of these sites corresponds often with that of regulatory elements in these genes as defined by mutations or, in the case of white, by molecular analysis. A zeste binding site is frequently found in the immediate vicinity of the promoter. zeste binding sites are composed of two or more zeste recognition sequences T/CGAGT/CG. Isolated consensus sequences do not bind or footprint. Cooperative interactions are involved both in binding to a given site and between proteins bound at independent sites. zeste bound to one DNA molecule can in fact bind simultaneously to another DNA molecule. These results suggest a general role for zeste in bringing together distant regulatory elements controlling the activity of a target gene. In this model, transvection effects are a by-product of normal intragenic zeste action.

Developmental expression of the Drosophila zeste gene and localization of zeste protein on polytene chromosomes

The expression of the zeste gene varies through the life cycle of the fly. Its transcription is most abundant in maternal RNA, declines to very low levels during larval growth, but rises again in late third instar larvae and pupae. Using transposons containing a zeste-lacZ gene, we found a corresponding variation in the tissue distribution of zeste from stage to stage. Nearly ubiquitous expression of the zeste-lacZ gene is found in late embryos and first instar larvae, but disappears almost completely except in brain and gonads by third instar larva. Shortly before pupation expression rises again in imaginal discs, Malpighian tubules, and salivary glands and again becomes nearly ubiquitous in pupae. zeste continues to be expressed in adult brain and gonads. We constructed flies carrying a zeste gene controlled by the heat shock promoter and studied the distribution of zeste protein in their polytene chromosomes as well as those of wild-type flies. Using affinity-purified anti-zeste antibodies, we find that wild-type salivary gland chromosomes contain about 60 strong bands of zeste immunofluorescence at specific cytological locations. After heat induction of larvae containing the hs-zeste gene, many hundreds of bands appear. These results suggest the involvement of zeste in the expression of a wide variety of genes at different developmental stages.

Zeste encodes a sequence-specific transcription factor that activates the Ultrabithorax promoter in vitro

Zeste is a Drosophila regulatory gene that is required for transvection at the bithorax complex. Here we find that purified zeste protein binds to multiple sites just 5' of the initiation site of Ubx RNA. Zeste protein purified from Drosophila cells or from E. coli expressing the zeste gene activates Ubx transcription in vitro. This activation is dependent on the presence of zeste protein binding sites, as it is not observed with a Ubx promoter lacking these sites or with an Adh promoter. These results suggest that transvection involves regulatory elements that act at the level of transcriptional initiation and may be mechanistically similar to activation of transcription by enhancer elements, except that transvection occurs across paired chromosomes. These findings are consistent with the hypothesis that zeste may play a more important role in the normal regulation of Ubx and its other target genes than current genetic evidence implies.

Microcloning reveals a high frequency of repetitive sequences characteristic of chromosome 4 and the beta-heterochromatin of Drosophila melanogaster

Microdissection and microcloning of the euchromatin-heterochromatin transition region of the Drosophila melanogaster polytene X chromosome and part of the euchromatin of chromosome 4 reveals that they share certain features characteristic of beta-heterochromatin, which is morphologically defined as the loosely textured material at the bases of some polytene chromosome arms. Both are mosaics of many different middle-repetitive DNA sequences interspersed with single-copy DNA sequences. Sixty percent of cloned inserts derived from division 20 and about 40 percent from subdivisions 19EF of the X chromosome harbor at least one repetitive DNA sequence in an average insert of 4.5 kilobases. No repeats have significant cross-hybridization to any of the eleven satellite DNAs, or to the clustered-scrambled sequences present in pDm1. The repetitive elements are, in general, confined to the beta-heterochromatic regions of polytene chromosomes, but some are adjacent to nomadic elements. Chromosome 4, however, has some repeats spread throughout its entire euchromatin. These data have implications for the structure of transition zones between euchromatin and heterochromatin of mitotic chromosomes and also provide a molecular basis for reexamining some of the unusual classical properties of chromosome 4.

The tko locus, site of a behavioral mutation in D. melanogaster, codes for a protein homologous to prokaryotic ribosomal protein S12

The tko (technical knockout) mutation is one of a family of behavioral mutations that cause "bang sensitivity" in D. melanogaster. Using P-element-mediated transformation, we show that a 3.1 kb piece of genomic DNA complements tko. This fragment contains only one complete transcript, 0.68 kb in length. This transcript is abundantly expressed through all stages of the life cycle, and we have isolated cDNAs corresponding to this transcript. Their sequence implies a protein product composed of 140 amino acids, which exhibits considerable sequence similarity to ribosomal protein S12 from both Euglena gracilis chloroplasts and E. coli. We suggest that tko codes for a mitochondrial ribosomal protein and that the tko phenotype results from defective mitochondria.

The product of the Drosophila zeste gene binds to specific DNA sequences in white and Ubx

Three different segments of the zeste coding sequence were inserted in an expression vector and antibodies were raised against the resulting zeste-beta galactosidase hybrid proteins. The antibodies were used to analyse the zeste protein produced in bacteria from a different expression vector containing the entire zeste coding region. The major products made in bacteria as well as the products of in vitro translation of zeste RNA migrate anomalously upon SDS--acrylamide gel electrophoresis. Specific DNA fragments from the white and Ubx gene co-immunoprecipitate with zeste protein. At least two independent zeste binding sites are found in a 250-bp interval of the white regulatory region that contains also the sites of wsp mutations, which are known to be deficient in zeste interaction.