Molecular and genetic studies on the euchromatin-heterochromatin transition region of the X chromosome of Drosophila melanogaster. 1. A cloned entry point near to the uncoordinated (unc) locus

Electron microscopic analysis of the banding pattern in the salivary gland chromosomes of Drosophila melanogaster. Divisions 11 through 20 of X

The banding pattern of the proximal half of the polytene salivary gland X chromosome of Drosophila melanogaster was studied using thin section electron microscopy. The bands were identified according to Bridges' revised light microscopic map. On Bridges' map, the divisions 11 to 20 contain 112 single bands and as many as 181 double bands. A majority of Bridges' single bands were identified in the thin sections. A total of 23 Bridges' single bands (and 4 bands of division 20) could not be found; in particular, bands were missing from the difficult regions 11DE, 15A, 15C and 16A. Electron microscopy showed the existence of 18 additional faint bands, 4 at the region 18D and 7 at 19EF. Bridges' faintest single bands and the new bands were best seen in formaldehyde fixed material. About 1/4 of Bridges' double bands were found to be made up of two separate bands each. The remaining Bridges' doublets include all kinds of bands: broad, narrow, dark, faint, puffed. Many of them look single in thin sections.

A 1.5 kb repeat sequence flanks the suppressor of forked gene at the euchromatin-heterochromatin boundary of the Drosophila melanogaster X chromosome

A 1.5 kilobasepair repeated DNA sequence is duplicated in direct orientation so as to flank the suppressor of forked gene in the euchromatin-heterochromatin transition region on the X chromosome of Drosophila melanogaster. These two copies are almost identical, but DNA blotting, analysis of cloned sequences and database searches show that elsewhere in the genome, homologous sequences are poorly conserved. They are often associated with other repeats, suggesting that they may belong to a scrambled and clustered middle repetitive DNA family. The sequences do not appear to be related to transposable elements and their location in different strains is conserved. In situ hybridization to metaphase chromosomes shows that homologous sequences are concentrated in the pericentric regions of the autosomes and the X chromosome. The sequences are not significantly under-represented in DNA from polytene tissue and must lie in the replicated regions of polytene chromosomes. The almost perfect conservation of the two repeats around suppressor of forked in D. melanogaster suggests they arose by duplication or gene conversion. Suppression of recombination in this chromosomal region presumably allows this unusual organization to be stably maintained. In the X-ray induced allele, suppressor of forked-L26, the sequence between the repeats, including the gene, and one copy of the repeat have been deleted.

Rates of movement of transposable elements in Drosophila melanogaster

Mobilization rates of nine families of transposable elements (P, hobo, FB, gypsy, 412, copia, blood, 297, and jockey) were estimated by using 182 lines. Lines were started from a completely isogenic population of Drosophila melanogaster, carrying the marker sepia as an indicator of possible contamination, and have been accumulating spontaneous mutations independently for 80 generations of brother-sister (or two double-first-cousin) matings. Transposable element movements have been analyzed in complete genomes by the Southern technique. Mobilization was a rare event, with an average rate of 10(-5) per site per generation. The most active element was FB. In contrast, the retroelements gypsy and blood did not move at all. Most changes in restriction patterns were consistent with rearrangements rather than with true transposition. The euchromatic or heterochromatic location of elements was tested by comparing insertion patterns from adults and salivary glands. Certain putative rearrangements involved heterochromatic copies of the retroelements 412, copia or 297. Clustering of movement across families was observed, suggesting that movement of different families may be non-independent. As association between modified insertion patterns and mutant effects on quantitative traits shows that spontaneous transposition events cause continuous variation.

Molecular and genetic dissection of a reproductive isolation gene, zygotic hybrid rescue, of Drosophila melanogaster

Hybrids from the cross between males of Drosophila melanogaster and females of its sibling species (D. simulans, D. mauritiana, or D. sechellia) are embryonic lethal when they carry the wild type allele of zygotic hybrid rescue (zhr) from D. melanogaster. The zhr gene has been mapped in the proximal region of the X heterochromatin slightly distal to the proximal breakpoint of In(1)sc8, the region rich in 1.688 g/cm3 satellite DNA. Since this satellite DNA does not exist in the sibling species, the satellite DNA was considered to be involved in the hybrid lethality. We examined the hypothesis molecular cytogenetically. The results are (1) three Df(1)zhr chromosomes carried this satellite DNA, and (2) hybrids were viable even if the amount of the satellite DNA in hybrids was increased by adding minichromosomes Dp(1;f)1205 and Dp(1;f)1187 into the genome. These results do not support the above hypothesis.

The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. III. Element abundances in heterochromatin

The total genomic copy numbers of ten families of transposable elements of Drosophila melanogaster in a set of ten isogenic lines derived from a natural population were estimated by slot-blotting. The numbers of euchromatic copies of members of each family were determined for each line by in situ hybridization of element probes to polytene chromosomes. Heterochromatic numbers were estimated by subtraction of the euchromatic counts from the total numbers. There was considerable variation between element families and lines in heterochromatic abundances, and the variance between lines for many elements was much greater for the heterochromatin than for the euchromatin. The data are consistent with the view that much of the beta-heterochromatin consists of sequences derived from transposable elements. They are also consistent with the hypothesis that similar evolutionary forces control element abundances in both the euchromatin and heterochromatin, although amplification of inert sequences derived from transposable elements may be in part responsible for their accumulation in heterochromatin.

Structure, molecular evolution and maintenance of copy number of extended repeated structures in the X-heterochromatin of Drosophila melanogaster

The 60 kb repeats located in the distal heterochromatin of the X chromosome of Drosophila melanogaster were cloned in overlapping cosmids. These regions, designated as SCLRs, comprised the following types of repeated elements: Stellate genes, which are known to be involved in spermatogenesis; copia-like retrotransposons; LINE elements, including amplified Type I rDNA insertions; and rDNA fragments. The following steps in SCLR formation were hypothesized: insertion of mobile elements into the rDNA and Stellate gene clusters; internal tandem duplication events; recombination between the rDNA cluster and Stellate tandem repeat; and amplification of the whole SCLR structure. There are about nine SCLR copies per haploid genome, but there is approximately a twofold variation in copy number between fly stocks. The SCLR copy number differences between closely related stocks are suggested to be the result of unequal sister chromatid exchange (USCE). The restricted variation in SCLR copy number between unrelated stocks and the absence of chromosomes free of SCLRs suggests that natural selection is active in copy number maintenance.

Homology with Saccharomyces cerevisiae RNA14 suggests that phenotypic suppression in Drosophila melanogaster by suppressor of forked occurs at the level of RNA stability

The suppressor of forked [su(f)] locus of Drosophila melanogaster encodes at least one cell-autonomous vital function. Mutations at su(f) can affect the expression of unlinked genes where retroviral-like transposable elements are inserted. Changes in phenotype are correlated with changes in mRNA profiles, indicating that su(f) affects the production and/or stability of mRNAs. We have cloned the su(f) gene by P-element transposon tagging. Alterations in the DNA map of eight lethal alleles were detected in a 4.3-kb region. P-element-mediated transformation using a fragment including this interval rescued all aspects of the su(f) mutant phenotype. The gene is transcribed to produce a major 2.6-kb RNA and minor RNAs of 1.3 and 2.9 kb, which are present throughout development, being most abundant in embryos, pupae, and adult females. The major predicted gene product is an 84- kD protein that is homologous to RNA14 of Saccharomyces cerevisiae, a vital gene where mutation affects mRNA stability. This suggests that phenotypic modification by su(f) occurs at the level of RNA stability.

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.

Nucleolus organizer-suppressed position-effect variegation in Drosophila melanogaster

The white locus is inactivated in a cell-by-cell variegated pattern when juxtaposed with the proximal or distal parts of the nucleolus organizer region (NO) by X chromosome inversion. Recombinants for two such inversions, wm51b and wm4, were obtained and randomized for genetic background. White locus activity was much higher in the wm4 recombinant duplicated for most of the NO and much lower in the wm51b recombinant deficient for it. Although there may be other molecular differences between the heterochromatic regions of the recombinants, the most obvious is the dosage of NO. Suppression of a NO region-evoked variegated phenotype by additional NO doses is discussed in relation to four different classes of models for position-effect variegation (PEV): chromatin structure, nuclear geometry, incomplete transposition of mobile elements, and heterochromatin promoter-driven transcription. A corollary of the structural model is functional subdivision of heterochromatin, which would enable the use of PEV as a tool for its study.

Cloning and characterization of the white and topaz eye color genes from the sheep blowfly Lucilia cuprina

Clones carrying the white and topaz eye color genes have been isolated from genomic DNA libraries of the blowfly Lucilia cuprina using cloned DNA from the homologous white and scarlet genes, respectively, of Drosophila melanogaster as probes. On the basis of hybridization studies using adjacent restriction fragments, homologous fragments were found to be colinear between the genes from the two species. The nucleotide sequence of a short region of the white gene of L. cuprina has been determined, and the homology to the corresponding region of D. melanogaster is 72%; at the derived amino acid level the homology is greater (84%) due to a marked difference in codon usage between the species. A major difference in genome organization between the two species is that whereas the DNA encompassing the D. melanogaster genes is free of repeated sequences, that encompassing their L. cuprina counterparts contains substantial amounts of repeated sequences. This suggests that the genome of L. cuprina is organized on the short period interspersion pattern. Repeated sequence DNA elements, which appear generally to be short (less than 1 kb) and which vary in repetitive frequency in the genome from greater than 10(4) copies to less than 10(2) copies, are found in at least two different locations in the clones carrying these genes. One type of repeat structure, found by sequencing, consists of tandemly repeating short sequences. Restriction site and restriction fragment length polymorphisms involving both the white and topaz gene regions are found within and between populations of L. cuprina.

A study of ten families of transposable elements on X chromosomes from a population of Drosophila melanogaster

Data were collected on the distribution of ten families of transposable elements among fourteen X chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization to polytene chromosomes. It was found that, with the exception of roo, the copy number per chromosome followed a Poisson distribution. There was no evidence for linkage disequilibrium, either within or between families. Some pairs of families of elements were correlated with respect to the identity of the sites that were occupied in the sample, although there was no evidence for a correlation with respect to the sites at which elements attained relatively high frequencies. Elements appeared to be distributed randomly along the distal part of the X chromosome. There was, however, a strong tendency for elements to accumulate at the base of the chromosome. Element frequencies per chromosome band were generally low, except at the base of the chromosome where bands in subdivisions 19E and 20A sometimes had high frequencies of occupation. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The accumulation of elements at the base of the chromosome is consistent with the idea that unequal exchange between elements at non-homologous sites is such a force, although other possibilities cannot be excluded at present. The data suggest that the rate of transposition per element per generation is of the order of 10(-4), for the elements included in this study.

On the role of unequal exchange in the containment of transposable element copy number

A population genetics model of the role of asymmetric pairing and unequal exchange in the stabilization of transposable element copy number in natural populations is proposed and analysed. Monte Carlo simulations indicate that the approximations incorporated into the analysis are robust in the relevant parameter ranges. Given several simple assumptions concerning transposition and excision, equal and unequal exchange, and chromosome structure, predictions of the relative numbers of transposable elements in various regions of theDrosophila melanogastergenome are compared to the observed distribution ofroo/B104elements across chromosomal regions with differing rates of exchange, and betweenXchromosomes and autosomes. There is no indication of an accumulation of elements in the distal regions of chromosomes, which is expected if unequal exchange is reduced concomitantly with normal crossing over in the distal regions. There is, however, an indication of an excess of elements relative to physical length in the proximal regions of the chromosomes, which also have restricted crossing over. This observation is qualitatively consistent with the model's predictions. The observed distribution of elements between the mid-sections of theXchromosomes and autosomes is consistent with the predictions of one of two models of unequal exchange.

Intercalary heterochromatin in Drosophila. III. Homology between DNA sequences from the Y chromosome, bases of polytene chromosome limbs, and chromosome 4 of D. melanogaster

Molecular and cytogenetic characteristics are given of a 2846 bp DNA sequence from the YDm12 clone, previously derived from the long arm of the Drosophila melanogaster Y chromosome. Sequence analysis revealed within it a 1176 bp fragment with 37 bp terminal inverted repeats, flanked by 6 bp direct repeats. This fragment (called "element 1360") appeared to be A-T rich, and was saturated with short direct and inverted repeats of different degrees of homology and consensus sequences for transcription, potential Z-DNA transition and autonomous replication. After in situ hybridization to polytene chromosomes, the element 1360 exhibited variable, strain-specifics location in the euchromatic parts of the chromosome arms, but constant heavy labelling of the X chromosome region 12E1-2, autosomal regions 42B1-3, 52A1-2, 62A1-2, 75B, 82C1-3, chromosome bases, the chromocentre and numerous sites of chromosome 4. The possible role of element 1360 in heterochromatin organization is discussed.

Molecular studies on interspersed repetitive and unique sequences in the region of the complementation group uncoordinated on the X chromosome of Drosophila melanogaster

The technique of chromosome walking was used to isolate approximately 60 kb of DNA from the region containing the complementation group uncoordinated of Drosophila melanogaster, located in that part of the X chromosome which spans the euchromatin-heterochromatin junction. The cloned DNA can be divided into two distinct regions. The first contains sequences that are low copy number or unique and are largely conserved between strains. The second region is characterized by units repeated in tandem arrays and is polymorphic within, and between, strains. Each repetitive unit is separated by a member of an abundant sequence family, part of which is homologous to the ribosomal type 1 insertion sequence of D. melanogaster. The molecular organization of the cloned DNA was compared with that of sequences isolated from regions of intercalary heterochromatin and also with genes which have been characterized from more conventional euchromatic regions.

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.

Restriction endonucleases variation in the region of the alcohol dehydrogenase gene: a comparison of null and normal alleles from natural populations of Drosophila melanogaster

The restriction endonuclease variation in the 12 kb region surrounding twelve Adh null alleles extracted from three Tasmanian populations has been compared with normal alleles from the same populations. Each of the null alleles had the same haplotype as revealed by digestions with eight hexanucleotide restriction enzymes. This haplotype also occurred in 4 of the 46 chromosomes bearing normal alleles which were tested; these four chromosomes with the null allele haplotype carried the AdhS allele. The data suggest that the Adh null alleles from geographically separate populations share a common ancestry and are derived from the same mutation in an AdhS allele.

The maintenance of transposable elements in natural populations

Models of the maintenance of transposable elements in randomly mating host populations are reviewed. It is shown that the data on the distribution of copy numbers between individuals are largely concordant with what is expected on the basis of the Mendelian transmission of elements. The role of regulation of rates of transposition, and of various modes of natural selection, in maintaining an equilibrium in copy numbers in the face of transpositional increase in copy number is discussed. Tests for the role of selection against insertional mutations and against chromosome rearrangements induced by exchange between homologous elements located at nonhomologous chromosome locations are discussed. Reasons for expecting elements to accumulate in chromosome regions where crossing over is restricted are discussed, and data suggesting the existence of such an effect are described. Theory and data on the probability distribution of element frequencies at individual chromosomal sites are described. It is concluded that the available population data are consistent with the notion that element abundances are largely controlled by the interaction of transpositional increase in copy number with opposing forces.

Localization of the genes shaking-B, small optic lobes, sluggish-A, stoned and stress-sensitive-C to a well-defined region on the X-chromosome of Drosophila melanogaster

Using deletion mapping and complementation tests, we have localized 5 behavioral mutations: shaking-B2, small optic lobesKS58, sluggish-AEE85, stonedts1, and stress-sensitive-C1 to 4 genetic complementation groups at the base of the X-chromosome. Shaking-B2 is an allele of the lethal complementation group R-9-29 near band 19E3; small optic lobesKS58 and sluggish-AEE85 belong to adjacent complementation groups, between lethals W2 and A112 near band 19F4; and stonedts1 and stress-sensitive-C1 are both alleles of the 8P1 lethal complementation group between lethals 114 and 13E3 near bands 20B-C.