Polytene Chromosome Bands Research Articles

The Drosophila suppressor of sable protein binds to RNA and associates with a subset of polytene chromosome bands.

Mutations of the Drosophila melanogaster suppressor of sable [su(s)] gene, which encodes a 150-kDa nuclear protein [Su(s)], increase the accumulation of specific transcripts in a manner that is not well understood but that appears to involve pre-mRNA processing. Here, we report biochemical analysis of purified, recombinant Su(s) [rSu(s)] expressed in baculovirus and in Escherichia coli as maltose binding protein (MBP) fusions and immunocytochemical analysis of endogenous Su(s). This work has shown that purified, baculovirus-expressed rSu(s) binds to RNA in vitro with a high affinity and limited specificity. Systematic evolution of ligands by exponential enrichment was used to identify preferred RNA targets of rSu(s), and a large proportion of RNAs isolated contain a full or partial match to the consensus sequence UCAGUAGUCU, which was confirmed to be a high-affinity rSu(s) binding site. An MBP-Su(s) fusion protein containing the N-terminal third of Su(s) binds RNAs containing this sequence with a higher specificity than full-length, baculovirus-expressed rSu(s). The consensus sequence resembles both a cryptic 5' splice site and a sequence that is found near the 5' end of some Drosophila transcripts. Immunolocalization studies showed that endogenous Su(s) is distributed in a reticulated pattern in Drosophila embryo and salivary gland nuclei. In salivary gland cells, Su(s) is found both in the nucleoplasm and in association with a subset of polytene chromosome bands. Considering these and previous results, we propose two models to explain how su(s) mutations affect nuclear pre-mRNA processing.

The Drosophila suppressor of sable protein binds to RNA and associates with a subset of polytene chromosome bands.

The Drosophila suppressor of sable protein binds to RNA and associates with a subset of polytene chromosome bands.

A Drosophila melanogaster homologue of the human DEAD-box gene DDX1

DEAD-box genes are found throughout evolution and encode RNA-binding proteins. Such proteins include eukaryotic initiation factor-4A, which is essential for protein translation, Vasa, which is essential for germ line development, and a number of nuclear and mitochondrial RNA splicing factors. Transcription of a human DEAD-box gene, DDX1, is elevated in two retinoblastoma cell lines as a result of amplificátion of the immediate chromosomal region surrounding it, suggesting an important role for this gene in control of cell growth and division. We have isolated a Drosophila melanogaster (Dm) homologue (Ddxl) of DDX1 which is strikingly similar to the human gene. The similarity (58.3% amino acid (aa) identity over 720 aa) extends beyond regions conserved in all DEAD-box proteins and covers the entire lengths of the proteins. The 2.7-kb Dm Ddxl RNA is expressed throughout development, but its levels are elevated in early embryos. Ddxl maps to polytene chromosome band 79D4 on the left arm of Dm chromosome 3.

Four new cytotypes of the onchocerciasis vector blackfly Simulium guianense in Brazil.

Simulium (Trichodagmia) guianense is an important Amazonian vector of onchocerciasis. Examination of the polytene chromosome banding patterns of larvae from five sites in Brazil revealed the occurrence of four cytotypes, designated A, B, C and D. The chromosomal standard, Simulium guianense A, occurred at two localities in Goias State (on the Rio Tocantins and Rio Mucambão) where it was the only cytotype. The other three sites examined yielded one different cytotype from each: B from Rio Oyapoque in Amapa State, C from Rio Tocantins in Maranhão State, and D from Rio Xingu in Para State. All cytotypes differed by at least two fixed inversions, but a sex determining system was not evident in any cytotype. As the cytotypes have been found allopatrically it is not certain that they represent sibling species; sampling of sympatric populations would resolve this. During certain times of the year, voracious anthropophagy by S.guianense sensu lato occurs at the localities sampled for cytotypes A, C and D (biting data are not available for the cytotype B locality). In some other areas, however, S.guianense s.l. is entirely zoophilic. Further studies are needed, therefore, to elucidate the biting habits, vectorial capacity, geographic distribution and taxonomic status of these four, and perhaps additional, cytotypes comprising the S.guianense complex.

Structural and functional properties of linker histones and high mobility group proteins in polytene chromosomes.

Variants of histone H1 and high mobility group (HMG) proteins and their genes in Dipteran insects are being studied in our laboratory and have revealed different properties of DNA binding and intrachromosomal distribution. One of the H1 variants of Chironomus is found only in a minority of polytene chromosome bands and differs from the other H1 proteins of the same organism by genomic organization and by an inserted structural motif, the KAPKAP repeat, that is present also in single H1 variants of other, evolutionarily remote organisms. NH2-terminal peptides containing the KAPKAP repeat were found in vitro to interact with DNA, whereas no DNA interaction was observed with the homologous peptide of another H1 variant that does not contain the inserted KAPKAP repeat. We assume that H1 variants containing the KAP motif may interact with a stretch of linker DNA and package chromatin more tightly than other H1 variants. A large series of antibodies directed against different sites in all regions of the H1 molecule is being applied in studying the sites of interaction of the H1 molecule with other molecules in interphase chromatin in terms of antibody epitope accessibility. A search for insect proteins that share properties of the mammalian HMG proteins resulted in isolation and sequencing of two different HMG1 proteins and an HMGI protein. The HMG1 protein of the midge, Chironomus tentans, show a differential distribution in chromosomes. The more abundant cHMG1a protein appears uniformly distributed, whereas the less abundant cHMG1b protein could be localized only in chromosomal puffs. This strongly indicates that these highly similar proteins have different functions in chromatin. The Chironomus HMGI protein and the intron/exon organization of its gene were found to be very similar to human HMGI/Y proteins that are highly abundant in rapidly proliferating cells. Common properties of HMG1 and HMGI proteins include high affinity interaction with AT-rich DNA, irregular DNA structures, and the capacity to bend DNA. These properties suggest that the HMG proteins may have an architectural role in assembling different types of chromatin.

A three-dimensional structural dissection of Drosophila polytene chromosomes.

We have analyzed the three-dimensional structural details of Drosophila melanogaster polytene chromosome bands and interbands using three-dimensional light microscopy and a novel method of sample preparation that does not involve flattening or stretching the chromosomes. Bands have been visualized in unfixed chromosomes stained with the DNA specific dye 4,6-Diamidino-2-phenylindole (DAPI). Interbands have been visualized using fixed chromosomes that have been immunostained with an antibody to RNA polymerase II. Additionally, these structures have been analyzed using in situ hybridization with probes from specific genetic loci (Notch and white). Bands are seen to be composed of approximately 36 substructural features that measure 0.2-0.4 micron in diameter. We suggest that these substructural features are in fact longitudinal fibers made up of bundles of chromatids. Band shape can be a reproducible characteristic of a particular band and is dependent on the spatial relationship of these bundles, varying from bands with a uniform distribution of bundles to bands with a peripheral concentration of chromatin. Interbands are composed of bundles of chromatids of a similar size and number as those seen in the bands. The distribution of bundles is similar between a band and the neighboring interband, implying that there is a long range organization to the DNA that includes both the coding and the noncoding portions of genes. Finally, we note that the polytene chromosome has a circular shape when viewed in cross section, whether there are one or two homologs present.

Molecular cloning of mei-41, a gene that influences both somatic and germline chromosome metabolism of Drosophila melanogaster.

The mei-41 gene of Drosophila melanogaster plays an essential role in meiosis, in the maintenance of somatic chromosome stability, in postreplication repair and in DNA double-strand break repair. This gene has been cytogenetically localized to polytene chromosome bands 14C4-6 using available chromosomal aberrations. About 60 kb of DNA sequence has been isolated following a bidirectional chromosomal walk that extends over the cytogenetic interval 14C1-6. The breakpoints of chromosomal aberrations identified within that walk establish that the entire mei-41 gene has been cloned. Two independently derived mei-41 mutants have been shown to carry P insertions within a single 2.2 kb fragment of the walk. Since revertants of those mutants have lost the P element sequences, an essential region of the mei-41 gene is present in that fragment. A 10.5 kb genomic fragment that spans the P insertion sites has been found to restore methyl methanesulfonate resistance and female fertility of the mei-41D3 mutants. The results demonstrate that all the sequences required for the proper expression of the mei-41 gene are present on this genomic fragment. This study provides the foundation for molecular analysis of a function that is essential for chromosome stability in both the germline and somatic cells.

Genetic mosaic analysis of the equatorial-less mutation in Drosophila melanogaster.

eql (equatorial-less) is a recessive lethal mutation on the second chromosome of Drosophila melanogaster. J. Campos-Ortega found that eql clones in somatic mosaic flies have reduced numbers of photoreceptor cells, and he suggested that only the R1, R6, and R7 photoreceptor cells were missing in this mutant. These photoreceptor cells help to define the inverted orientation of ommatidial facets along the equatorial midline of the fly eye, hence the mutation was named "equatorial-less." We have conducted a detailed analysis of the eql mutation, by serial section reconstruction of eql clones marked with bw- or w- in somatic mosaic flies. We found that all photoreceptor cell types (R1-R8) could be deleted by the eql mutation, and in rare cases the number of photoreceptor cells was increased. The apparent lack of photoreceptor cell type specificity was confirmed by our analysis of genetically mosaic facets, which indicated that no single photoreceptor cell, or subset of photoreceptor cells, was uniquely required to express eql+. Rather, eql appears to function in all photoreceptor cells, and possibly in all eye precursor cells. The distribution of photoreceptor cell numbers in w eql facets was consistent with the hypothesis that each photoreceptor cell was deleted independently of the others. The eql gene is located on the right arm of chromosome 2 at map location 2-104.5 +/- 0.7 and lies between the polytene chromosome bands 59D8 and 60A7.

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.

Immunofluorescent localization of nuclear protein in polytene chromosomes of two chironomid species:Endochironomus tendens(Fabr.) andGlyptotendipes gripekoveniKieffer (Diptera, Chironomidae)

SUMMARYA monoclonal antibody (Mab 2a8) has been generated against a DNA tight binding protein of eukaryotic cells. Its distribution was investigated in salivary gland polytene chromosomes of two Chironomid species, Endochironomus tendens and Glyptotendipes gripekoveni, by immunofluorescence. The results indicate: 1. Mab 2a8 is distributed in some distinct condensed bands along the entire lenght of chromosomes; 2. The banding pattern obtained with fluorescent antibody does almost strictly correspond to some Hoechst positive bands and to constitutive heterochromatin sites established by «C» banding method. Other condensed (Hoechst positive) bands on chromosomes were Mab 2a8 immunonegative. 3. No immunofluorescent was observed in genetically active regions of polytene chromosomes (puffs, Balbiani rings and nuclear organizer). The mode of distribution in defined bands of polytene chromosomes suggests the residence of this protein in polytene chromosomes, whose presence appears to be well in correlation with t...

Anopheles hermsi, probable vector of malaria in New Mexico.

Samples of Anopheles freeborni s.1. were collected from areas of New Mexico where malaria had once been common and sporozoites had been isolated from this species. Specimens were identified by analysis of polytene chromosome banding patterns and by specific rDNA fragments generated through the polymerase chain reaction. All samples collected in New Mexico were identified as An. hermsi, which was the probable vector of malaria in this region during the early 20th century.

The isolation and characterization of a Drosophila gene encoding a putative NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase

Mammalian NAD-dependent 5,10-methylenetetrahydrofolate dehydrogenase-5,10-methenyltetrahydrofolate cyclohydrolase is a bifunctional mitochondrial enzyme expressed in most established cell lines but only in developing normal tissues. We report the cloning and molecular characterization of a Drosophila gene ( DNMDMC) that encodes a protein with 56% identity to the mammalian bifunctional protein. Like the mammalian bifunctional proteins, the Drosophila protein contains a putative mitochondrial targeting sequence and its transcripts are expressed in developing tissues. Unlike its mammalian homologs, DNMDMC is expressed at high levels in adult tissues. DNMDMC maps to polytene chromosome band 85C, is encoded in three exons, and is closely flanked by two additional genes.

Laboratory colonization of Anopheles quadriannulatus from sympatry with other sibling species of the Anopheles gambiae complex in Zimbabwe

A laboratory colony of the mosquito Anopheles quadriannulatus was established from a wild population occurring sympatrically with An.arabiensis in Zimbabwe. These sibling species are members of the An.gambiae Giles complex and were distinguished primarily by means of their specific polytene chromosome banding patterns. By using an ox-baited trap, we sampled selectively for the more zoophilic An.quadriannulatus. It was confirmed that An.quadriannulatus has the diagnostic slow allozyme of aspartate aminotransferase (AAT95/95). In a mixed population under laboratory conditions, An.arabiensis displaced An.quadriannulatus within eight generations, without introgression. Colonization of An.quadriannulatus was facilitated by pooling the progeny from wild-caught mothers of confirmed identity and by using a specially adapted cage to promote mating.

Genetic instability in Drosophila melanogaster mediated by hobo transposable elements.

Eight independent recessive lethal mutations that occurred on derivatives of an unstable X chromosome (Uc) in Drosophila melanogaster were analyzed by a combination of genetic and molecular techniques. Seven of the mutations were localized to complementation groups in polytene chromosome bands 6E; 7A. In situ hybridization and genomic Southern analysis established that hobo transposable elements were associated with all seven of the mutations. Six mutations involved deletions of DNA, some of which were large enough to be seen cytologically, and in each case, a hobo element was inserted at the junction of the deletion's breakpoints. A seventh mutation was associated with a small inversion between 6F and 7A-B and a hobo element was inserted at one of its breakpoints. One of the mutant chromosomes had an active hobo-mediated instability, manifested by the recurrent production of mutations of the carmine (cm) locus in bands 6E5-6. This instability persisted for many generations in several sublines of an inbred stock. Two levels of instability, high and basal, were distinguished. Sublines with high instability had two hobo elements in the 6E-F region and produced cm mutations by deleting the segment between the two hobos; a single hobo element remained at the junction of the deletion breakpoints. Sublines with low instability had only one hobo element in the 6E-F region, but they also produced deletion mutations of cm. Both types of sublines also acquired hobo-mediated inversions on the X chromosome. Collectively, these results suggest that interactions between hobo elements are responsible for the instability of Uc. It is proposed that interactions between widely separated elements produce gross rearrangements that restructure the chromosome and that interactions between nearby elements cause regional instabilities manifested by the recurrence of specific mutations. These regional instabilities may arise when a copy of hobo transposes a short distance, creating a pair of hobos that can interact to produce small rearrangements.

Cytogenetic analysis of chromosome region 89A of Drosophila melanogaster: isolation of deficiencies and mapping of Po, Aldox-1 and transposon insertions.

We have initiated a cytogenetic analysis of chromosome region 89A of Drosophila melanogaster by isolating a set of radiation-induced mutations causing loss of function of P[(w)B]1-1, a transposon bearing the white locus inserted in 89A. Complementation tests and cytological examination of these chromosomes identified four new deficiencies (Df(3R)Po2, Df(3R)Po3, Df(3R)Po4 and Df(3R)c(3)G2). The new deficiencies and three previously identified deficiencies (Df(3R)sbd26, Df(3R)sbd45 and Df(3R)sbd105) were tested for the ability to complement mutations in the enzyme loci Po and Aldox-1, the indirect flight muscle genes Tm2 and act88F, the morphological mutations jvl, sbd2 and Sb, the vital loci srp, pnr and mor, and a newly described vital locus l(3)89Aa. We also used linkage analysis to determine the order and relative positions of P[(w)B]1-1 and an independent transposon insertion, P[w+]21, with respect to cv-c, Po, Aldox-1 and sbd2. Cytological examination of the deficiencies and analysis of the transformed lines by in situ hybridization permits the correlation of genetically defined regions with specific polytene chromosome bands. A revised cytogenetic map of the 88F-89B region is presented.

Molecular analysis of the lethal(1)B214 region at the base of the X chromosome of Drosophila melanogaster.

Approximately 50 kb of genomic DNA was isolated from polytene chromosome bands 19F1 and 2 of Drosophila melanogaster. Bands 19F1 and 2 are in the immediate vicinity of the beta-heterochromatin at the base of the X chromosome and encompass the little fly-like and lethal(1)B214 complementation groups. The cloned DNA consists of an approximately 21 kb stretch of unique or low copy number sequence that is bounded by repetitive elements interspersed with further unique sequences. The presence of repeated sequences is characteristic of regions within and adjacent to beta-heterochromatin. At least part of a tRNA gene cluster is present within the 50 kb of cloned DNA. The cloned region also produces at least 18 discrete size classes of developmentally regulated poly(A)+ RNA species. A 2 kb EcoRI fragment (E10), which lies in the 21 kb stretch of unique sequence, generates seven of these transcripts (of sizes 3.5, 3.35, 2.1, 2.0, 1.5, 1.2 and 1.0 kb) in wild-type flies. However, a small deletion of approximately 75 bp in E10 in a lethal(1)B214 mutant allele is associated with alterations in the production or processing of all seven of these transcripts. These data identify E10 sequences as belonging to the lethal(1)B214 gene and suggest that the wild-type lethal(1)B214 gene encodes multiple transcripts. Furthermore, no transcripts of the same size and having the same developmental profile as those generated by the wild-type E10 fragment were identified by probes covering the remainder of the cloned region. This suggests that at least the larger transcripts hybridizing to E10 are partly transcribed from sequences located outside the cloned region, which indicates that the lethal(1)B214 gene extends for more than 20 kb and contains other transcriptionally active sequences within it.

A polytene chromosome study of four populations of Anopheles aquasalis from Venezuela.

Polytene chromosome studies were undertaken to elucidate taxonomic relationships among populations of Anopheles aquasalis and A. emilianus in Venezuela. Four collection sites were chosen: two in Sucre state (Santa Fe and Guayana) where A. aquasalis (considered to be A. emilianus by Gabaldón and Escalante) is presumed to be the major regional vector of Plasmodium vivax; and two in areas where no malaria transmission occurs (Caño Rico, Aragua state, and Puerto Cabello, Carabobo state). The chromosome banding pattern of the four populations was identical and conformed to the standard chromosome map of A. aquasalis from Brazil. These results suggest that the population from Santa Fe and Guayana, considered to be A. emilianus, is conspecific with A. aquasalis. However, its status as a distinct species with a homosequential polytene chromosome banding pattern cannot be ruled out.

Genetic and developmental analysis of polytene section 17 of the X chromosome of Drosophila melanogaster.

Polytene section 17 of the X chromosome of Drosophila melanogaster, previously known to contain six putative lethal complementation groups important in oogenesis and embryogenesis, has here been further characterized genetically and developmentally. We constructed fcl+Y, a duplication of this region, which allowed us to conduct mutagenesis screens specific for the region and to perform complementation analyses (previously not possible). We recovered 67 new lethal mutations which defined 15 complementation groups within Df(1)N19 which deletes most of polytene section 17. The zygotic lethal phenotypes of these and preexisting mutations within polytene section 17 were examined, and their maternal requirements were analysed in homozygous germline clones using the dominant female sterile technique. We present evidence that an additional gene, which produces two developmentally regulated transcripts, is located in this region and is involved in embryogenesis, although no mutations in this gene were identified. In this interval of 37 to 43 polytene chromosome bands we have defined 17 genes, 12 (71%) of which are of significance to oogenesis or embryogenesis.

Species-specific differences in tissue-specific expression of alcohol dehydrogenase are under the control of complexcis-acting loci: Evidence fromDrosophila hybrids

Differences in the expression of alcohol dehydrogenase in the hindgut and testis of adult Drosophila virilis, D. texana, D. novamexicana and D. borealis flies were observed. These heritable differences do not arise due to chromosomal rearrangements, since the polytene chromosome banding patterns did not reveal any such gross chromosomal rearrangements near the Adh locus in any of the tested species. Analysis of the interspecific hybrids revealed that these differences are controlled by complex cis-acting genetic loci. Further, the cis-acting locus controlling the expression of ADH in testis was found to be separable by crossing-over.

Comparison of mitochondrial DNA sequences of seven morphospecies of black flies (Diptera: Simuliidae)

Universal primers constructed from the 16S ribosomal RNA gene in the Drosophila yakuba mitochondrial genome were successfully used to amplify, via the polymerase chain reaction, the homologous region of mitochondrial DNA from seven black fly morphospecies. Amplification was achieved from single larval salivary glands and from single adults preserved in Carnoy's fixative (ethanol - acetic acid, 3:1), allowing DNA sequences and polytene chromosome banding pattern data to be gathered from the same individuals. Nucleotide sequences of the amplified DNA segment (347 base pairs) were obtained from all the species examined. As in Drosophila, the nucleotide base composition of the sequenced segment from black flies had a high adenine (A) and thymine (T) content (A + T on average comprised 77% of all nucleotides.). Nucleotide differences among the seven species were observed at 59 positions (55 nucleotide substitutions and 4 deletions). There were more transversion differences than transition differences both among and within genera; the proportion of transversions was higher between genera than within genera. Most transversion differences were A----T type, comprising 79% of all transversion differences and 50% of all sequence differences. Phylogenetic inference based strictly on transversion differences confirmed traditional generic and tribal groupings, i.e., Prosimulium fuscum (Syme & Davies) is close to Prosimulium magnum (Dyar & Shannon); Simulium decorum (Walker), Simulium venustum s.l. (Say), and Simulium vittatum s.l. (Zetterstedt) are close to each other; Stegopterna mutata (Malloch) and Cnephia dacotensis (Dyar & Shannon), which belong to the tribe Cnephiini, are grouped together.