Polytene Bands Research Articles

Reverse genetics of Drosophila RNA polymerase II: identification and characterization of RpII140, the genomic locus for the second-largest subunit.

We have used a reverse genetics approach to isolate genes encoding two subunits of Drosophila melanogaster RNA polymerase II. RpII18 encodes the 18-kDa subunit and maps cytogenetically to polytene band region 83A. RpII140 encodes the 140-kDa subunit and maps to polytene band region 88A10:B1,2. Focusing on RpII140, we used in situ hybridization to map this gene to a small subinterval defined by the endpoints of a series of deficiencies impinging on the 88A/B region and showed that it does not represent a previously known genetic locus. Two recently defined complementation groups, A5 and Z6, reside in the same subinterval and thus were candidates for the RpII140 locus. Phenotypes of A5 mutants suggested that they affect RNA polymerase II, in that the lethal phase and the interaction with developmental loci such as Ubx resemble those of mutants in the gene for the largest subunit, RpII215. Indeed, we have achieved complete genetic rescue of representative recessive lethal mutations of A5 with a P-element construct containing a 9.1-kb genomic DNA fragment carrying RpII140. Interestingly, the initial construct also rescued lethal alleles in the neighboring complementation group, Z6, revealing that the 9.1-kb insert carries two genes. Deleting coding region sequences of RpII140, however, yielded a transformation vector that failed to rescue A5 alleles but continued to rescue Z6 alleles. These results strongly support the conclusion that the A5 complementation group is equivalent to the genomic RpII140 locus.

Dense Cluster of Genes is Located at the Ecdysone-regulated 3C Puff of Drosphila melanogaster

The 3C11-12 polytene bands of the Drosophila melanogaster X chromosome give rise to a prominent puff, whose regression is triggered by the increase in the titre of the steroid hormone 20-hydroxyecdysone occurring before the metamorphosis. Here, we report the molecular characterization of three genes, named ng-2, ng-3 and ng-4, which we found to be closely linked to each other and to Sgs-4, Pig-1 and ng-1, three other genes previously mapped at this polytene region. All six genes are, in fact, arranged in a tightly linked cluster spanning a DNA segment of only 11 kb. With the exception of ng-4, all the clustered genes are highly expressed only during the larval life and share the same tissue-specificity, being mainly transcribed within the salivary glands. In addition, two members of the cluster, ng-1 and ng-2, show a very high degree of sequence homology, clearly indicating that they are related to each other by means of a duplication event. Interestingly to note, the entire cluster shows a peculiar genomic location, extending across two introns of the memory gene dunce, a large gene of Drosophila whose organization has proved to be remarkably complex.

Effect of ecd1 mutation on the expression of genes mapped at the Drosophila melanogaster 3C11-12 intermoult puff.

The Drosophila melanogaster ecd1 mutation causes a severe temperature-sensitive deficiency in the titre of the steroid hormone ecdysone. This mutation was used to investigate the role of ecdysone in both the transcription of the genes mapped at the 3C11-12 intermoult puff region and the puff formation. Thoroughly synchronized ecd1 larvae were shifted to the non-permissive temperature at various times of the development; after 24 or 48 h, the levels of the transcripts derived from Sgs-4, Pig-1 and ng-1, the three genes located at the 3C11-12 polytene bands, were determined. The results showed that the levels of the transcripts encoded by Pig-1 and ng-1 are unaffected by the drop in the ecdysone titre occurring in non-permissive conditions whereas the amount of Sgs-4 mRNA is greatly reduced. These data clearly indicate that transcription of the three genes mapped within the puff region is affected differently by the hormone. Furthermore, ecd1 larvae cultured at the non-permissive temperature show a prominent puff at the 3C11-12 polytene bands, indicating that ecdysone is not essential for puff induction and that puff size is not simply correlated with high-level Sgs-4 transcription.

Molecular organization of the Drosophila melanogaster Pig-1 gene

The Pre-intermoult gene-1 (Pig-1) of Drosophila melanogaster maps on the X chromosome, at polytene bands 3C11-12, and is nested within the 79 kb intron of the dunce gene. Pig-1 has so far been characterized only preliminarily and its function is still unknown. We analysed the molecular organization of the gene by cDNA clone isolation and sequencing as well as S1 mapping and primer extension analyses. The results obtained reveal that the gene is colinear with its genomic sequence and define the usage of both 5' and 3' alternative sites for Pig-1 transcription; two continuous open reading frames (ORFs) are fully contained within the Pig-1 transcribed region, although several lines of evidence suggest that only the longer ORF is likely to be translated. We also report that the level of Pig-1 transcript is nearly fourfold reduced in a variant strain carrying a deletion within the Pig-1 upstream sequence, thus identifying a regulatory element required for high level gene expression.

A cluster of four genes selectively expressed in the male germ line of Drosophila melanogaster

The gene Mst87F is exclusively expressed in the male germ line and is subject to translational regulation. The Mst87F mRNA is transcribed in the primary spermatocytes, stored for three days and then subsequently translated in the post-elongation period of spermiogenesis. Here we report on the isolation of a cluster of four small genes closely related in structure and function to Mst87F. These genes are located at polytene band 84D on the right arm of chromosome three and are named Mst84Da, Mst84Db, Mst84Dc and Mst84Dd. All four genes encode putative proteins composed primarily of a repetitive motif of cysteine-glycine-proline. The genes are exclusively expressed in the male germ line. The poly(A) tail of the Mst84D mRNAs increases in length at day three of pupal development, the time at which a similar change in Mst87F mRNA and translation has been shown to begin. In addition we have identified a conserved 12 base pair element within the 5′ untranslated region (UTR) of each gene which is also found at an identical position in Mst87F and which has been demonstrated to be the structural element for translational control of Mst87F expression (Schäfer et al., 1990 EMBO J. 9, 4519–4525). We have mapped the gene cluster to a small deletion associated with a rotund mutation at 84D. Although flies with a homozygous deletion of the cluster still produce motile sperm, electron microscopic examination revealed numerous malformations in the ultrastructure of the axoneme resulting in a drastic reduction of motile sperm.

Segregation Distortion in Drosophila melanogaster: Genetic and Molecular Analyses

The Segregation Distorter (SD) complex in the centromeric region of chromosome 2 in Drosophila melanogaster is responsible for a naturally occurring and strong system of male meiotic drive. Earlier recombinational dissection and deletional analysis showed that the SD complex resolves into three major loci: the euchromatic Sd, or Segregation distorter gene at the base of the left arm of the chromosome (2L), and two heterochromatic genes: E(SD), the Enhancer of SD, and Rsp, the Responder, in the center of the left arm and the right arm (2R), respectively. Rsp exists in the major allelic forms, RsPs, for sensitive, and Rspi, for insensitive. Males that are heterozygous for an SD chromosome (SdE(SD)Rspi) and a sensitive SD+ homologue (Sd+E(SD)+Rsps) transmit predominantly or even exclusively the SD-bearing chromosome to the progeny. The distortion of the segregation ratio is traceable to failure in chromatin condensation and maturation of those spermatids that receive the Rsps homologue during meiosis. Characterization of the properties of null alleles of Sd, E(SD), and Rsp that were generated by deletion determined the precise cytological locations of the components and established the functional relationship of each to its wild-type counterpart, suggesting a model whereby a deleterious action of Sd, along with E(SD), on the Rsps target sets in motion the events culminating in sperm dysfunction. Further genetic analysis of E(SD), a gene required for full expression of drive, showed that E(SD) in two doses can cause significant distortion even in the absence of Sd. This distortion is suppressible by a suppressor of SD action. Thus, E(SD) is more than a simple modifier of Sd; rather, it is an effector locus that, like Sd, can act at the Rsps target. Cloning and molecular analysis of the Sd locus reveal that the alteration uniquely associated with Sd is a 5-kb tandem duplication within the polytene band 37D5, which is where Sd is known to map. The Sd-associated duplication appears to be part of a large gene about 100 kb in size. A 4.2-kb SD-specific transcript has been identified, and analyses of the cDNAs indicate a complex transcription pattern. Since Responder plays such a key role in segregation distortion, recent progress in analyzing this locus has been exciting. Studies of Rsp at the genetic, cytogenetic, and molecular levels have been mutually reinforcing and consistent in demonstrating that Rsp is an extended locus that is (1) subdivisible and (2) associated with a 120-bp repeated sequence of DNA that is rich in adenine-thymine pairs and whose copy number is correlated with the degree of sensitivity. In an exceptional situation, there are certain SdRspi/Sd+ Rsps males cartying particular modifiers in which the Rspi chromosome can he transmitted at frequencies of less than 0.50 relative to the Rsps chromosome, suggesting that the genetics of segregation ratios may involve even further complexities, which need to be unraveled.

The Passover locus in Drosophila melanogaster: complex complementation and different effects on the giant fiber neural pathway.

Drosophila melanogaster bearing the Passover mutation fail to jump in response to a light-off stimulus. Pas also disrupts some of the synapses between the neurons of the giant fiber system which mediate this escape behavior. We have mapped Pas to the 19E subdivision of the polytene X chromosome. Our genetic analyses reveal that deletions of either of two nonoverlapping regions fail to fully complement Pas. Heterozygotes of Pas with chromosomal deletions in the vicinity of polytene band 19E3 exhibit the full set of neuronal defects shown by Pas homozygotes. Alleles of the R-9-29 complementation group, which maps to band 19E3, exhibit a complex pattern of complementation with Pas. Heterozygotes combining the lethal R-9-29 alleles with Pas are all viable, some complement the neuronal defects of Pas, but most exhibit these defects. The viable shaking-B2 mutation also fails to complement Pas, the R-9-29 alleles or the 19E3 deficiencies. The R-9-29 locus may contain two functional domains, one required for viability the other for normal neuronal phenotype, trans-Heterozygotes bearing mutant alleles or a deficiency of the first region (19E3) together with deficiencies of the second region (19E5-6) also exhibit some of the neuronal defects shown by the Passover mutant. Deficiencies which delete the entire 19E3 to 19E6 interval do not produce this phenotype when heterozygous with a normal X chromosome. Thus normal function requires a cis-interaction between the two regions. These findings raise the possibility that the gene mutated by Pas is split or separated from a cis-activator by at least one other gene.

The exuperantia gene is required for Drosophila spermatogenesis as well as anteroposterior polarity of the developing oocyte, and encodes overlapping sex-specific transcripts.

The Drosophila gene exuperantia (exu) is a maternal effect gene which is needed for proper localization of the bcd RNA during the formation of oocytes. We have extended the characterization of the exu phenotype and find that the gene functions in the male as well as the female germline. Six of seven exu alleles are male-sterile; mutant defects in spermatogenesis first appear during meiosis. A genetic analysis presented here shows that the exu gene does not encode a zygotic vital function. The isolation of two overlapping deficiencies that delete exu function localizes the gene cytologically to polytene bands 57A4-B1. We describe the molecular cloning and identification of the gene, and show that it encodes overlapping sex-specific transcripts of 2.9 kb in the male and 2.1 kb in the female. We also show that these two transcripts are limited in expression to the germline. We demonstrate that one allele, exuVL57, is a deletion of about 700 bp which results in a loss of both transcripts.

Cytogenetic analysis of chromosome region 73AD of Drosophila melanogaster.

The 73AD salivary chromosome region of Drosophila melanogaster was subjected to mutational analysis in order to (1) generate a collection of chromosome breakpoints that would allow a correlation between the genetic, cytological and molecular maps of the region and (2) define the number and gross organization of complementation groups within this interval. Eighteen complementation groups were defined and mapped to the 73A2-73B7 region, which is comprised of 17 polytene bands. These complementation groups include the previously known scarlet (st), transformer (tra) and Dominant temperature-sensitive lethal-5 (DTS-5) genes, as well as 13 new recessive lethal complementation groups and one male and female sterile locus. One of the newly identified lethal complementation groups corresponds to the molecularly identified abl locus, and another gene is defined by mutant alleles that exhibit an interaction with the abl mutants. We also recovered several mutations in the 73C1-D1.2 interval, representing two lethal complementation groups, one new visible mutant, plucked (plk), and a previously known visible, dark body (db). There is no evidence of a complex of sex determination genes in the region near tra.

Sequence homology between a polytene band in the genetic sex chromosomes ofChrysomya rufifacies and thedaughterless gene ofDrosophila melanogaster

Sequence homology between a polytene band in the genetic sex chromosomes ofChrysomya rufifacies and thedaughterless gene ofDrosophila melanogaster

A chromosomal walk in the region of polytene bands 7C-D of theDrosophila X chromosome

A chromosomal walk on the X chromosome ofDrosophila in the region of polytene bands 7C1 to 7D5 is described. The region is of interest since three olfactory genes have been found to map here in addition to a haplo-inviable locus. Genomic clones spanning 160 kilobases have been isolated and their complete restriction map is presented. The clones have been aligned on the polytene chromosome bands byin situ hybridisation. In addition the end-points of a deficiency and duplication lying in this region have been mapped approximately, showing that an overlap exists between them.

Developmental genetics of loci at the base of the X chromosome of Drosophila melanogaster.

We have conducted a genetic and developmental analysis of the 26 contiguous genetic complementation groups within the 19D3-20F2 interval of the base of the X chromosome, a region of 34 polytene bands delimited by the maroon-like and suppressor of forked loci. Within this region there are four loci which cause visible phenotypes but which have little or no effect on zygotic viability (maroon-like, little fly, small optic lobes and sluggish). There are 22 loci which, when mutated, are zygotic lethals and three of these, legless/runt, folded gastrulation and 13E3, have severe effects on embryonic development. In addition, three visible phenotypes have been defined only by overlapping deficiencies (melanized-like, tumorous head, and varied outspread). We have analyzed the lethal phases and maternal requirement of 58 mutations at 22 of the zygotic lethal loci by means of germline clone analysis using the dominant female sterile technique. Additionally, all lethal complementation groups, as well as a specific subset of deficiencies, have been studied histologically for defects in the development of the central and peripheral embryonic nervous systems.

Drosophila vitelline membrane genes contain a 114 base pair region of highly conserved coding sequence

Two Drosophila vitelline membrane (VM) genes located at polytene band positions 26A and 34C have been characterized at the nucleotide level. Sequence comparison of the two genes VM26A.1 and VM34C.1 has revealed a similar 114 base pair region centrally located in the coding regions of both genes. The conserved region has a 91% homology at the nucleic acid level and a 100% conservation at the amino acid level. This suggests a common evolutionary origin for these VM genes and indicates that a strong selective pressure exists to maintain a specific polypeptide sequence in a domain of the proteins.

Precise determination of the molecular limits of a polytene chromosome band: Regulatory sequences for the Notch gene are in the interband

We have aligned the molecular map of the North locus to the cytological features of the salivary gland polytene chromosomes of D. melanogaster in order to determine the interphase chromatin structure of this gene. Using high-resolution in situ hybridization and computer-aided optical microscope data collection and image analysis, we have determined that the coding portions and introns of the Notch gene, which is not expressed in this tissue, are all contained within the polytene chromosome band 3C7. The portion of the Notch gene that resides 5′ to the start of transcription lies in an open chromatin conformation, the interband between bands 3C6 and 3C7. Our data are most consistent with condensation of the chromosomal DNA into 30 nm fibers in this polytene band.

The instability of the TE-like mutation Dp(2:2)GYL of Drosophila melanogaster is intimately associated with the hobo element.

We have characterized molecularly several derivatives of the TE-like element Dp(2:2)GYL of Drosophila melanogaster. This highly unstable mutation occurred in a dysgenic cross involving the 23.5 MRF chromosome, and represents an inverted insertional duplication of approximately 130 polytene bands of the paternal 2L, at 50AB of the right arm of the maternal 2R. The instability of this mutation is characterized by deletion of some of duplicated material, by the induction of rearrangements in its vicinity and by the transposition of parts of the original element. We have found that the mobile element hobo is present at , or very near, the breakpoints of all GYL derivatives analysed, demonstrating that hobo is not only active in dysgenic crosses, but also that it can promote genetic instability reminiscent of transposable elements (TE).

Isolation and chromosomal location of putative vitelline membrane genes in Drosophila melanogaster.

cDNA clones for two Drosophila vitelline membrane genes have been identified on the basis of: (i) stage and tissue specificity of transcription and (ii) size and amino acid content of the translation product. Cross-hybridization data suggest that DmcMM99 and DmcMM115 are members of a multi-gene family which includes at least three members, all of which reside on the left arm of the second chromosome. DmcMM99 and DmcMM115 originate from polytene band positions 34C and 26A, respectively. A third, cross-hybridizing gene resides at position 32EF. Southern analysis of a genomic clone, lambda LS1, homologous to DmcMM115, indicates that two vitelline membrane genes may be clustered at the 26A site.

Genetic analysis of the sexual dimorphism of glass inDrosophila melanogaster

SUMMARYA modifier locus is described that alters the level of phenotypic expression of the third chromosome mutant glass in a sex specific manner. Alternative alleles either confer a sexually dimorphic level of pigment in glass mutants, with the male being greater, or cause similar expression in the two sexes. The alleles are indistinguishable in females but produce the respective phenotypes in males. The gene maps to the tip of theXchromosome at position 0·96 ± 0·11. Cytologically, the locus is present between polytene bands 3A6–8 and 3C2–3 as determined by its inclusion in translocatedXsegments inw+Y,Dp(l;2)w70h31andDp(l;3)w67k27The dimorphic allele is dominant to the nondimorphic condition in males heterozygous for an insertional translocation carrying the dimorphic allele and a normal chromosome carrying the nondimorphic form. The dimorphic allele in two doses in males does not exhibit a dosage effect. The modifier phenotype is unaffected in twoXflies by the presence of the transformer mutation.

Apparent resistance to mutagenesis by ionizing radiation, and some other unusual responses.

It is pointed out that in some species it is very difficult or even apparently impossible to get genetic visible marker mutants by means of ionizing radiation. Such results are not as a rule published. Species in which no mutants at all could be obtained, after what seem to be adequate efforts by several geneticists are Limnaea peregra, Rhynchosciara angelae, Coelopa frigida, Oncopeltus fasciatus, Dermestes maculatus. Published data on Sciara, Tribolium, Blattella, in which a relative difficulty in getting mutants is reported, are discussed and compared to many other forms in which obtaining marker mutants is on the contrary easy. What appears to be very abnormal mutagenesis is described in Drosophila busckii, which yielded an unusual frequency of autosomal dominants, and Drosophila nebulosa, in which only very poor mutants could be obtained. Possible reasons for all these departures from the usual are discussed. No firm conclusions are reached, but one is led to consider the possible effects of overall chromosome structure, presence or absence of heterochromatin, and multiplicity at the single locus or single polytene band level. There seems to be no relation between the rates of induction of dominant lethality and of point mutation for visible markers.

HISTONE GENE MULTIPLICITY AND POSITION EFFECT VARIEGATION IN DROSOPHILA MELANOGASTER

The histone genes of wild-type Drosophila melanogaster are reiterated 100-150 times per haploid genome and are located in the segment of chromosome 2 that corresponds to polytene bands 39D2-3 to E1-2. The influence of altered histone gene multiplicity on chromatin structure has been assayed by measuring modification of the gene inactivation associated with position effect variegation in genotypes bearing deletions of the 39D-E segment. The proportion of cells in which a variegating gene is active is increased in genotypes that are heterozygous for a deficiency that removes the histone gene complex. Deletions that remove segments adjacent to the histone gene complex have no effect on the expression of variegating genes. Suppression of position effect variegation associated with reduction of histone gene multiplicity applies to both X-linked and autosomal variegating genes. Position effects exerted by both autosomal and sex-chromosome heterochromatin were suppressible by deletions of the histone gene complex. The suppression was independent of the presence of the Y chromosome. A deficiency that deletes only the distal portion of the histone gene complex also has the ability to suppress position effect variegation. Duplication of the histone gene complex did not enhance position effect variegation. Deletion or duplication of the histone gene complex in the maternal genome had no effect on the extent of variegation in progeny whose histone gene multiplicity was normal. These results are discussed with respect to current knowledge of the organization of the histone gene complex and control of its expression.

Cytogenetic localization by variation in electrophoretic allozyme phenotype: Drosophila Odh

A gene-dosage effect is characteristic of eukaryotic structural genes and is therefore useful in gene mapping. However, attributing quantitative variations in enzyme activity to a gene-dosage effect or other putative regulatory loci can be suspect when the locus in question may be inducible by variations in culture conditions. The problem of controlling for allele-specific variations in activity and regulation can be circumvented in Drosophila melanogaster by the use of synthetic duplications and deficiencies in conjunction with enzyme polymorphism. A method for constructing segmental aneupliods heterozygous for electrophoretic variants of octanol dehydrogenase (Odh) is presented which permitted variations in allozyme phenotype and enzyme activity--which show a strict dosage dependency--to be produced simultaneously. The structural gene region for Odh was identified using T(Y;A) stocks and the deficiency M(3)S31 was used to assign the locus to polytene band region 86D1-4. With this method a segmental aneuploid survey of Drosophila for purposes of gene localization can be accomplished in one generation with appropriate stocks.