Physical map of the white locus of Drosophila melanogaster

Molecular and phenotypic variation of the white locus region in Drosophila melanogaster

Restriction site and insertion/deletion polymorphism in a 45-kb region of the white locus on the X chromosome in Drosophila melanogaster was investigated for 64 X chromosome lines with six 6-cutter and ten 4-cutter restriction enzymes. A total of 109 polymorphisms were detected (54 restriction sites and 55 insertions/deletions). Estimated heterozygosity per nucleotide for this region (0.004-0.008) was similar to those of the Adh and 87A heat-shock locus regions located on the autosomes in D. melanogaster. This is contrary to a simple prediction based on the theory of mutation selection-balance of partially recessive deleterious mutants which predicts less variation on X chromosomes. Large linkage disequilibria between pairs of polymorphisms (including insertions and deletions) within the transcriptional unit (especially the 3' end of the 1st intron) were observed. As expected from population genetics theory, linkage disequilibria between these polymorphisms were greater for those pairs that are physically closer on the restriction map. Linkage equilibrium was typically observed when the pairs of sites were separated by 2 kb or more. Although significant between-line variation in eye pigment was observed (P less than 0.05), there is little evidence for strong associations between this phenotype and the polymorphisms at the DNA level.

P element insertions and rearrangements at the singed locus of Drosophila melanogaster

DNA from the singed gene of Drosophila melanogaster was isolated using an inversion between a previously cloned P element at cytological location 17C and the hypermutable allele singed-weak. Five out of nine singed mutants examined have alterations in their DNA maps in this region. The singed locus is a hotspot for mutation during P-M hybrid dysgenesis, and we have analyzed 22 mutations induced by P-M hybrid dysgenesis. All 22 have a P element inserted within a 700-bp region. The precise positions of 10 P element insertions were determined and they define 4 sites within a 100-bp interval. During P-M hybrid dysgenesis, the singed-weak allele is destabilized, producing two classes of phenotypically altered derivatives at high frequency. In singed-weak, two defective P elements are present in a "head-to-head" or inverse tandem arrangement. Excision of one element results in a more extreme singed bristle phenotype while excision of the other leads to a wild-type bristle phenotype.

Partial revertants of the transposable element-associated suppressible allele white-apricot in Drosophila melanogaster: structures and responsiveness to genetic modifiers

The eye color phenotype of white-apricot (wa), a mutant allele of the white locus caused by the insertion of the transposable element copia into a small intron, is suppressed by the extragenic suppressor suppressor-of-white-apricot (su(wa] and enhanced by the extragenic enhancers suppressor-of-forked su(f] and Enhancer-of-white-apricot (E(wa]. Derivatives of wa have been analyzed molecularly and genetically in order to correlate the structure of these derivatives with their response to modifiers. Derivatives in which the copia element is replaced precisely by a solo long terminal repeat (sLTR) were generated in vitro and returned to the germline by P-element mediated transformation; flies carrying this allele within a P transposon show a nearly wild-type phenotype and no response to either su(f) or su(wa). In addition, eleven partial phenotypic revertants of wa were analyzed. Of these, one appears to be a duplication of a large region which includes wa, three are new alleles of su(wa), two are sLTR derivatives whose properties confirm results obtained using transformation, and five are secondary insertions into the copia element within wa. One of these, waR84h, differs from wa by the insertion of the most 3' 83 nucleotides of the I factor. The five insertion derivatives show a variety of phenotypes and modes of interaction with su[f) and su(wa). The eye pigmentation of waR84h is affected by su(f) and E(wa), but not su(wa). These results demonstrate that copia (as opposed to the interruption of white sequences) is essential for the wa phenotype and its response to genetic modifiers, and that there are multiple mechanisms for the alteration of the wa phenotype by modifiers.

Insertional DNA and spontaneous mutation at the white locus in Drosophila simulans

A large body of data on molecular analyses of several multiallelic loci in Drosophila melanogaster has demonstrated a high incidence of mobile DNA element insertions among spontaneous mutations. In the sibling species D. simulans, the dispersed, middle repetitive, nomadic sequences are reduced to about one-seventh that of its sibling species (Dowsett and Young 1982). Does this reduced amount of middle repetitive DNA (or mobile DNA sequences) mean that in D. simulans the occurrence of insertion mutants will be rare compared with that of D. melanogaster? To test this possibility, we collected seven different spontaneous white mutants of D. simulans and studied their molecular gene structures. Five out of seven mutants had insertion sequences which varied in length from 0.4 kb to 16 kb. One bore a deletion spanning the w region and another showed no gross structural alteration. Thus the proportion of insertional mutations at the white locus in D. simulans is equivalent to that observed in D. melanogaster. Among the five insertional mutants, one, wmky, showed genetic instability; the other four were stable. wmky was found to mutate at a frequency of 2.1 x 10(-5) in meiotic cells and may also be unstable in somatic cells.

Asymmetrical pairings of transposons in and proximal to the white locus of Drosophila account for four classes of regularly occurring exchange products

An explanation for the origins of four classes of regularly occurring duplication and deficiency chromosomes is provided through examination of their molecular structures. The duplications and deficiencies occur as the reciprocal products of crossing-over, following two different patterns of asymmetrical synapsis between transposons positioned in and proximal to the white locus of Drosophila melanogaster. Three copies of the retrovirus-like transposon roo are involved in the exchanges. Evidence suggests that transposon-mediated asymmetrical exchange is a general phenomenon in eukaryotes, which adds significantly to the effects of transposons in the restructuring of eukaryotic genomes.

Differential riboflavin deposition in white and variegated white mutants of Drosophila hydei

Riboflavin deposition in organs of Drosophila hydei was studied by means of a growth test using a riboflavin-deficient strain of the fungus Aspergillus nidulans. In wild-type animals, riboflavin is deposited in Malpighian tubules (MT) and testes but not in adult eyes. Certain white (w) mutants do not contain riboflavin, whereas intermediately colored w mutants contain minor amounts of the substance. Riboflavin-containing MT cells contain special globules that can be fixed and stained with the redox dye phenazine-methosulphate. The number and size of these granules is related to growth effect and point to a role of the w locus in the intracellular deposition of riboflavin in special organs. In white-mottled (wm) position-effect variegation mutants, a significant correlation was found between the extent of variegation (percentage of yellow cells) and riboflavin content (growth effect) of the MT. However, the individual variation of cell phenotype was extremely large and exaggerated types were observed indicating "overdominance" of the rearranged w+ gene. This contradicts an unsubstantiated dogma of position-effect variegation that assumes that the affected gene simply switches between the on and off state, as is discussed.

Molecular structure of a somatically unstable transposable element in Drosophila

A transposable element has been isolated from an unstable white mutation in Drosophila mauritiana, a sibling species of Drosophila melanogaster. The unstable white-peach (wpch) allele exhibits a spectrum of germ-line and somatic mutability more similar to insertion mutations in maize and in the nematode Caenorhabditis elegans than has been reported for insertion mutations in Drosophila. The inserted element mariner is 1286 nucleotides long and has terminal inverted repeats. The element contains a single open reading frame encoding 346 amino acids. A duplication of 2 base pairs of white sequence is present at the insertion site. Mariner is present in approximately 20 copies in the D. mauritiana genome, is present from 0 to 7 copies in other members of the sibling species group, and is apparently absent from the genome of D. melanogaster.

Genetic-molecular basis for a simple Drosophila melanogaster somatic system that detects environmental mutagens

We have developed a simple, objectively scorable test for the mutagenicity of chemical compounds which can be fed Drosophila melanogaster. The test depends upon the somatic reversion of the X chromosome, recessive eye color mutation, white-ivory (wi) to wild type (w+). Reversions are scored as clones of w+ facets in the wi eyes of eclosing adults. To increase the sensitivity, a tandem quadruplication containing four wi mutations was synthesized. Thus, in homozygous females eight wi mutations are potentially revertible. Six mutagenic compounds, all alkylating agents, all gave positive results at several concentrations tested. Molecular analysis demonstrates that the induced reversions, germinal and somatic, are associated with the loss of 2.9-kilobase DNA duplicated in the wi mutation.

Molecular cloning, germ-line transformation, and transcriptional analysis of the zeste locus of Drosophila melanogaster

Approximately 170 kilobase pairs (kb) of contiguous DNA sequences derived from bands 3A3,4 of the Drosophila melanogaster X chromosome have been isolated by molecular cloning. Sequences required for the wild-type expression of the zeste locus are located within a 6-kb fragment of this chromosomal region, as shown by phenotypic rescue of zeste mutants in P element-mediated germ-line transformation. Expression of zeste is correlated with a 2.2-kb poly(A)+ RNA species transcribed at all postzygotic stages of Drosophila development. Many zeste alleles, including several producing neomorphic phenotypes, are not associated with detectable rearrangements of DNA.

Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

Genetic and physical studies of a portion of the white locus participating in transcriptional regulation and in synapsis-dependent interactions in Drosophila adult tissues

We have identified and sequenced the portion of the white locus affected by an idiosyncratic set of white mutant alleles (the wsp alleles). The affected white locus portion (wsp region) extends from ca. 590 base pairs (bp) to ca. 1270 bp 5' to the apparent start site for the major white transcription unit. Based on the properties of these mutant alleles, we infer the existence of two distinct cis-acting regulatory elements in the wsp region and a third element mapping 3' to this region (3' to position ca. -670). Our analysis allows us to define the apparent position of one of the two wsp region elements with substantial precision. Examination of the DNA sequences in this region suggests that it is functionally similar to the enhancers identified in vertebrates. This same element participates in synapsis-dependent genetic interactions, suggesting a largely unexpected relationship between enhancer-like, cis-acting genetic elements and the genetic elements responsible for the synapsis-dependent genetic interactions in trans revealed by the existence of transvection effects. Our results further suggest that a presumptive regulatory locus (suppressor-of-white-spotted) regulates white transcription in adult tissues and is not involved in regulating white expression in larvae. We discuss the regulation of white expression in light of our studies. We also demonstrate unusual structures for an X-ray-induced deletion and a spontaneous deletion.

Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

Excision of copia element in a revertant of the white-apricot mutation of Drosophila melanogaster leaves behind one long-terminal repeat

The spontaneous mutation white-apricot (wa) in Drosophila melanogaster has a considerably lighter eye colour than the wild-type, and is caused by the insertion of a copia transposable element into a small intron of the white gene. We have analyzed an X-ray induced wa revertant (waR59K1), whose eye pigmentation is incompletely restored, by in situ hybridization, Southern blotting and sequencing analysis. At the site where copia had originally inserted, we found one long terminal repeat of copia, flanked by a 5 bp duplication with the same polarity as the direction of transcription of the white locus. These results suggest that the wa reversion is due to homologous recombination between the two long terminal repeats of copia.

Structure of chromosomal rearrangements induced by the FB transposable element in Drosophila

Examination of 10 chromosomal rearrangements induced by foldback transposable elements in Drosophila demonstrates that sequences located between two closely linked elements are frequently deleted. Rearrangement and recombination events occurring within or adjacent to a foldback element are also observed. The type and frequency of rearrangement generated depend on element structure and the organization of flanking DNA.

Vectors for P element-mediated gene transfer in Drosophila

We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D. melanogaster. The P element in one vector also carries the rosy gene which serves as an easily scored marker to facilitate the transfer of DNA fragments that do not themselves confer a recognizable phenotype. The failure of certain P element constructs to function as vectors suggests that P element sequences, in addition to the 31 bp inverse terminal repeats, are required in cis for transposition. Moreover, removal of the first 38 bp of the autonomous 2.9 kb P element appears to destroy its ability to provide a trans-acting factor (s) required for the transposition of non-autonomous P elements. Finally, we describe a genomic sequence arrangement that apparently arose by the transposition of a 54 kb composite P element from a tetramer plasmid.

Association of a Drosophila transposable element of the roo family with chromosomal deletion breakpoints

A 9.3 kb transposable element of the roo family has been found inserted 3' to the Sgs-4 glue protein gene of Drosophila. The X chromosome which carries this insert also carries wDZL, a dominant, unstable allele of the white locus caused by the insertion of the 13 kb wDZL element. Three deletions isolated from the wDZL strain have molecular breakpoints 3' to Sgs-4 that are associated with the roo element. Though the deletions eliminate much of the DNA between white and Sgs-4, none of the distal breakpoints fall at or near the wDZL element. The results suggest that this copia-like element, which is structurally similar to an integrated retrovirus, is capable of promoting chromosomal deletions.

Chromosome sorting and DNA sequence localization

This article focuses on current techniques and possible future developments in chromosome isolation and sorting, and DNA analysis of sorted chromosomes. The strategy of subchromosomal gene mapping by chromosome sorting is outlined and a list of cell lines containing translocated chromosomes is provided which may be used to map genes to a single chromosome with a standard fluorescence activated cell sorter. The usefulness of this and other gene mapping methods for localizing unique DNA sequences and characterizing recombinant DNA libraries constructed from sorted chromosomal DNA is also discussed.