Hoppel-family of mobile elements of Drosophila melanogaster, flanked by short inverted repeats and having preferential localization in the heterochromatin regions of the genome

A mobile element (ME) having 91% homology with Dm1360 (Kholodilov et al., 1987) has been cloned from the Drosophila melanogaster genome and sequenced. The family of ME was designated hoppel. The members of this family are flanked by short inverted repeats likewise P, hobo and HB. The hoppel is hybridized with 10-30 euchromatic sites of polytene chromosomes of different Drosophila stocks. Abundant hybridization with heterochromatic regions of chromosomes-chromocenter, pericentric heterochromatin, the 4 chromosome and telomeres was observed in all stocks of D. melanogaster examined and in D. simulans. At least six genomic variants of ME differing in length of the central part were revealed. Hoppel possesses ARS activity similar to the P element. Two ME hoppel were shown to be arranged as a direct repeat in the recombinant phage.     

He-T family DNA sequences in the Y chromosome of Drosophila melanogaster share homology with the X-linked Stellate genes

The genome of Drosophila melanogaster contains a class of repetitive DNA sequences called the He-T family, which is unusual in being confined to telomeric and heterochromatic regions. The specific He-T fragment designated Dm665 was cloned in yeast by selection for an autonomously replicating sequence (ARS). Dm665 contains a restriction fragment length polymorphism (RFLP) that is specific to males and thus derives from the Y chromosome. Deletion mapping using X-Y translocations indicates that sequences homologous to Dm665 occur in at least one major cluster in each arm of the Y chromosome. Among 20 yeast artificial chromosome (YAC) clones containing Drosophila sequences homologous with Dm665, four clones derive from defined regions of the long arm of the Y and two from the short arm. The sequence of Dm665 is 2443 bp long, consists of 59% A+T, and contains no significant open reading frames or direct or inverted repeats. However, Dm665 contains a region of 650 bp that shares homology with portions of the X-linked locus Stellate.by W. Hennig     

Heterochromatic regions in different Drosophila melanogaster stocks contain similar arrangements of moderate repeats with inserted copia-like elements (MDG1)

Seven out of twenty 30–50 kb genome fragments with an MDG1 copia-like element cloned in cosmids were found to carry homologous sequences which belong to a new family of non-mobile heterochromatic moderate repeats (the HMR family). These repeats along with the MDG1 copies inserted in them are under-replicated in polytene chromosomes. Such repeats may also be located in the intercalary heterochromatin site 12E of the X chromosome. Chromosomal heterochromatic regions are enriched with one of the two main genomic variants of MDG1, MDG1^het, identifiable by EcoRI restriction. From Southern DNA blot analysis the number of MDG1^het copies and their sites within the heterochromatin are invariant in all the stocks examined, while there is not a single MDG1 site along the polytene chromosomes shared by all the stocks in question.     

The Heterochromatic ABO Locus May Overlap with the Region Containing Repeats Encompassing Mobile Elements andStellate Genes on the X Chromosome of Drosophila melanogaster

A deficiency of certain heterochromatic regions (ABO loci) of various chromosomes dramatically distorts the early embryo development in the progeny of females carrying mutation in the abnormal oocyte (abo) gene, which is located in euchromatin of chromosome 2. One ABO locus (X-ABO) is in X-heterochromatin distal to the nucleolus organizer. A cluster of the Stellate repeats is located in the same heterochromatic block. Deletions of various fragments from distal heterochromatin were tested for the effect on expression of the abo mutation. The X-ABO locus was assigned to X-chromosomal heterochromatin segment h26 and may include repeats consisting mostly of mobile elements and defective Stellate copies. A major part of the regular Stellate tandem repeats proved to be distal of the X-ABO locus.     

Molecular and genetic studies on the euchromatin-heterochromatin transition region of the X chromosome of Drosophila melanogaster

A recombinant Charon 4 bacteriophage has been isolated on the basis of RNAs which are enriched in the head of the adult Drosophila melanogaster and hence are likely to be of neural origin. The cloned insert maps to the near vicinity of the uncoordinated locus in polytene chromosome band 19E8. This band is within the transition zone between the euchromatic and heterochromatic regions of the X chromosome, a region which has been well characterized cytogenetically. The insert contains both repetitious and low copy number sequences, some of which vary extensively in both frequency and restriction fragment size between different laboratory strains. One particular family of moderately repeated sequences occurs predominantly in divisions 19 and 20 of the X chromosome and perhaps the distally located X heterochromatin. The molecular landscape surrounding the initial entry point contains many repeated sequences and is thus unlike those observed in most published chromosomal walks. The possible significance of the presence of repeated sequence families in the distinct properties of this region are discussed.     

Cytogenetic characterization of the 4BC region on the X chromosome of Drosophila melanogaster: Localization of the mei-9, norpA and omb genes

Thirty genetic alterations, which involve the 4BC region of the Drosophila X chromosome, have been induced by ionizing radiation or by an endogenous mutator element. These mutations were recovered by screening for reversion of the dominant mutants Oce and Qd or for induction of the recessive mutants bi and rb. Among the 23 mutants generated by ionizing radiation, 20 have proven to be cytologically detectable chromosomal aberrations. Seven additional unique aberrations were generated in the Uc mutator strain. In total, 22 cytologically detectable deficiencies, 3 translocations, 1 inversion, 1 transposition, and 3 cytologically normal mutants have been recovered. Complementation analysis has permitted the cytogenetic localization of eight genes in the 4BC region. The mei-9 locus has been assigned to region 4B4-6, because this function is carried by Df (1)rb ⁴¹ but not by Df(1)bi ^D1. The norpA locus has been placed in the 4B6-C1 region based on its location between the distal breakpoints of Df(1)bi ^D2 and Df(1)rb ⁴¹. The genes lac, Qd, bi, and omb are localized to bands 4C5,6, rb to 4C6 and amb to 4C7,8. With one exception the complementation analysis has also permitted a determination of the linear sequence of these genes. This cytogenetic localization of these loci will facilitate the cloning and molecular analysis of genes controlling a key function in DNA repair and recombination (mei-9), and two fundamental neural functions (norpA and omb).     

An X chromosome locus in Drosophila melanogaster that enhances survival of the triplo-lethal genotype,Dp-(Tpl)

Only a single locus (Tpl) is known in the Drosophila melanogaster genome that leads to early lethality when present as a heterozygous duplication (three doses) or deficiency (one dose). We report the recovery of third instar larvae (and of occasional adults) carrying a duplication for the triplo-lethal locus, Dp(Tpl). Karyotype analysis of the larvae showed that the individuals surviving were almost entirely 3X;2A metafemales. We examined the question of whether the entire X or a single X locus was a major factor permitting survival. X-Y translocations were used to produce females hyperploid for different portions of the X and carrying Dp(Tpl). Analysis of metaphase chromosomes by quinacrine fluorescence pattern indicates that the X chromosome region between 6D and 7DE must be present in an extra copy to enhance the survival of Tpl duplication-bearing females. Another type of experiment suggests that it is the region between 7C and 7DE which is essential.     

The centric region of the X chromosome rDNA functions in male meiotic pairing in Drosophila melanogaster

In Drosophila melanogaster males, sex chromosome pairing at meiosis is ensured by so-called pairing site(s) located discretely in the centric heterochromatin. The property of the pairing sites is not well understood. Recently, an hypothesis has been proposed that 240 bp repeats in the nontranscribed spacer region of rDNA function as the pairing sites in male meiosis. However, considerable cytogenetic evidence exists that is contrary to this hypothesis. Hence, the question is whether the chromosomal rDNA clusters, in which a high copy number of 240 bp repeats exists, are involved in the pairing. In order to resolve the problem we X-rayed Drosophila carrying the X chromosome inversion In(1)sc ^V2L sc ^8R and generated free, mini-X chromosomes carrying a substantial amount of rDNA. We defined cytogenetically the size of the mini-chromosomes and studied their meiotic behavior. Our results demonstrate that the heterochromatin at the distal end of the inversion, whose length is approximately 0.4 times that of the fourth chromosome, includes a meiotic pairing site in the male. We discuss the cytological location of the pairing site and the possible role of rDNA in meiotic pairing.     

Mobile elements and transposition events in the cut locus of Drosophila melanogaster

We have cloned from the Oregon R strain of Drosophila melanogaster a 240 kb segment of DNA that contains the cut (ct) locus, and characterized the region for the presence of repetitive elements. Within this region at least five copies of the suffix element were detected, as well as several putatively novel mobile elements. A number of mutations obtained from the unstable ct ^MR2 strain and its derivatives were mapped within the cut locus. Comparison between parental and daughter strains indicates that frequently two or more independent transposition events involving the cut locus occur simultaneously within a single germ cell, thus providing a molecular basis for the transposition explosion phenomenon.     

The effect of X chromosome heterozygosity on the structure of the ribosomal genes in Drosophila melanogaster.

Sucrose gradient analysis of DNA isolated from detergent-pronase lysates of adult flies has been used to look for ribosomal genes not integrated into the DNA of the chromosome in genotypes containing various combinations of inversions having breakpoints in the proximal heterochromatin of the X chromosome. Unintegrated genes are found in females heterozygous for inversions which have one breakpoint between the nucleolus organizer and the centromere. Homozygotes and males do not have unintegrated genes. The results suggest that unintegrated ribosomal genes result from an interaction between homologues having different arrangements of the proximal heterochromatin. In addition, data from a series of stocks carrying duplications of the X heterochromatin provide independent evidence for the size of the DNA on our gradients.     

The meiotic behavior of some single-cistron mutants in the zeste-white region of the Drosophila melanogaster X chromosome

Summary There are two dosage sensitive sites in the zeste-white region of the Drosophila melanogaster X chromosome that affect meiotic chromosome behavior. Single-cistron mutants at essential and female fertility loci in the two segments have been tested for meiotic effects similar to those of deficiencies. None of the mutants have detectable meiotic effects. A de novo search for meiotic mutants in the region has not uncovered any, but the results suggest that a deficiency for the zeste-white region would be useful for detecting meiotic mutants elsewhere in the genome. Tests for interactions between the deficiency and known meiotic mutants support this. Though tentative, these results suggest that non-essential regions need not be devoid of function.Research supported by National Science Foundation grant PCM 79-01824     

Polymorphism of the Mdg-1 and I mobile elements in Drosophila melanogaster

The polymorphism of the mobile elements Mdg-1 (a copia-like element) and I (an element involved in I-R hybrid dysgenesis) was analysed in a mass-mated population of Drosophila melanogaster by in situ hybridization, using biotinylated DNA probes, on polytene chromosomes. The Mdg-1 and I elements were inserted independently but were within the same bulk of DNA insertion points of the Drosophila genome, which contained on average about 30 insertion sites for each element. The X chromosome contained the lowest copy number of elements while 2R and 3R had the highest number: 3R had the highest variability. There was no correlation between the copy numbers of elements among the chromosome arms. The average expected per locus heterozygosity was equal to 0.17 for both the Mdg-1 and the I elements. Although these two elements differ in sequence, they appeared to behave similarly in the Drosophila melanogaster genome. This suggests that they may compete for target insertion sites and may be under the same control mechanisms.     

Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome

The recent sequencing of several eukaryotic genomes has generated considerable interest in the study of gene duplication events. The classical model of duplicate gene evolution is that recurrent mutation ultimately results in one copy becoming a pseudogene, and only rarely will a beneficial new function evolve. Here, we study divergence between coding sequence duplications in Drosophila melanogaster as a function of the linkage relationship between paralogs. The mean K(a)/K(s) between all duplicates in the D. melanogaster genome is 0.2803, indicating that purifying selection is maintaining the structure of duplicate coding sequences. However, the mean K(a)/K(s) between duplicates that are both on the X chromosome is 0.4701, significantly higher than the genome average. Further, the distribution of K(a)/K(s) for these X-linked duplicates is significantly shifted toward higher values when compared with the distributions for paralogs in other linkage relationships. Two models of molecular evolution provide qualitative explanations of these observations-relaxation of selective pressure on the duplicate copies and, more likely, positive selection on recessive adaptations. We also show that there is an excess of X-linked duplicates with low K(s), suggesting a larger proportion of relatively young duplicates on the D. melanogaster X chromosome relative to autosomes.     

Cloning and characterization of variable-sized gypsy mobile elements in Drosophila melanogaster

A cosmid genomic library from a known gypsy-induced forked mutation, f1, was screened by 32P-labeled gypsy transposable element. Of more than 250 positive clones we randomly selected 21 for in situ hybridization to wild-type polytene chromosomes. Two clones hybridized to region 15F on the X-chromosome, the cytological position of forked. A third clone hybridized to at least 17 sites on the chromosomes indicating the presence of repetitive sequences in the gypsy flanking DNA. All clones labeled the centromeric regions heavily. Ten clones, including the two hybridizing at 15F, were chosen for further analysis, and restriction mapping allowed us to place them into three groups: (1) full-length, (2) slightly diverging, and (3) highly diverging gypsy elements. Group (2) is missing the XbaI site in both their long terminal repeats (LTRs) as well as the middle HindIII site; four of these gypsy elements also have a approximately 100-bp deletion at the 5' LTR. The group (3) gypsy transposons are missing one LTR and also have highly diverging DNA sequences. The restriction analyses further imply that most of these different gypsy elements are present in more than one copy in the genome of the f1 stock used in this study. The results raise intriguing questions regarding the significance of transposable elements in evolution and biological functions.     

Distribution of Drosophila melanogaster mobile genetic elements along X-chromosome and autosomes

The distribution along Drosophila melanogaster polytene X-chromosome and autosomes of 10911 in situ hybridization sites of a broad spectrum of copialike mobile elements is investigated. It is shown that against DNA content X-chromsomal cytological sections 14 + 15 and 16 + 17 contain much less mobile elements than other chromosomal regions. These X-chromosomal regions are also characterized both by significant decrease in the meiotic recombination frequencies and the amount of poly(dC-dA).poly(dG-dT) sequences which are capable to generate the Z form of DNA.