High-frequency precise excision of the Drosophila foldback transposable element

Precise excision of transposable elements in prokaryotes is a rare event which occurs at a significantly lower rate than transposition and other element-mediated events. Thus, we were intrigued by a eukaryotic transposable element which seemed capable of precise excision at high frequencies. The white-crimson (wc) mutation in Drosophila, a highly unstable allele of the X-linked eye colour locus, white, resulted from the insertion of a member of the foldback (FB) transposable element family. This mutation reverts to its parental phenotype at a frequency of greater than 1 in 10(3) X chromosomes. Characterization of these revertants by Southern blots of genomic DNA indicated that they resulted from loss of the wc insertion. Here we report the nucleotide sequence of the excision point in these revertants, and conclude that the FB element responsible for the wc mutation is capable of precise excision at high frequencies.     

Similarity of the Cin1 repetitive family of Zea mays to eukaryotic transposable elements

It has been suggested that the middle repetitive class of sequences that make up a large proportion of the eukaryotic genome have been amplified and dispersed by DNA transposition. Transposition is a phenomenon first postulated by Barbara McClintock on the basis of her genetic analysis of mutants in Zea mays. Since then, DNA transposition has been studied genetically in various plant systems and is well documented on the molecular level in both prokaryotes and eukaryotes. This has included the isolation of DNA inserts at various loci in several plants; however, the prevalence of transposition in plants is not established. We report here DNA nucleotide sequence data which show that some members of the Cin1 middle repetitive family of maize have features characteristic of known transposable elements. One cloned Cin1 repeat has a 6-base pair (bp) perfect inverted repeat sequence at its ends. The terminal five base pairs (5' TGTTG . . . CAACA 3') are identical to the termini of Drosophila copia transposable elements. Two other Cin1 alleles are flanked by 5-bp direct repeats. A comparison is made with the long terminal repeat (LTR) of the copia-Ty1-retrovirus families of moveable genetic elements.     

Transposon-dependent mutant phenotypes at the Notch locus of Drosophila

Many mutations at complex genetic loci in the fruitfly Drosophila melanogaster are associated with insertions of transposable elements. At the Notch locus, members of one class of insertion-associated mutations, termed glossy-like, produce a recessive viable, smooth-eye phenotype with mottled pigmentation. Members of a second class, facet, produce a recessive viable, rough-eye phenotype with homogeneous pigmentation. Both classes of mutations fail to complement Notch lethal mutations, so they behave as Notch alleles. Here we report that each glossy-like mutation is associated with an insertion of the same transposable element (flea). Each flea insertion occurs in the same orientation, but at different locations within intervening sequences of the Notch locus. In contrast, each facet mutation is associated with insertion of a unique, non-flea, transposable element. Insertions producing a facet phenotype and insertions causing a glossy-like phenotype can break Notch intervening sequences at precisely the same location. This suggests that the type of insertion element rather than its position within an affected gene is the primary determinant of the phenotype observed.     

Genetic effects of injection of Rous sarcoma virus DNA into polar plasm of early Drosophila melanogaster embryos

Retroviral proviruses and the transposable elements of eukaryotic genomes are structurally similar. The biological significance of eukaryotic transposable elements has not been examined extensively but it is known that, like prokaryotic transposons, these elements can induce mutations in adjacent genes and cause their transposition. It is of interest to determine whether retroviral proviruses have the same mutagenic and gene transposing ability as transposable elements, particularly because the retrovirus genome is assumed to have originated from transposable elements of lower eukaryotes. The transfer of DNA sequences into animal zygotes or embryos by microinjection is a promising experimental approach for eluxidating their functions: when foreign DNAs were introduced into a mouse germ line, mutations were induced and at least in some mice, the mutation was caused by the insertion of a retroviral sequence. We have introduced Rous sarcoma virus (RSV) DNA into a germ line of Drosophila melanogaster, and describe here the resultant genetic effects.     

Transposition of Tn554 does not generate a target duplication

Transposable elements from prokaryotic and eukaryotic organisms are discrete DNA segments bounded by inverted or directly repeated sequences that insert into non-homologous DNA in a reaction that is independent of the general recombination functions of the host. The mechanisms proposed generally involve a staggered double-stranded scission of the target DNA, ligation to the nicked ends of the transposable element, and replication of the element, resulting in the generation of a directly repeated oligonucleotide target sequence flanking the new copy of the element. Most transposons have a relatively low degree of target site specificity coupled with a low insertion frequency. Tn554, a Staphylococcus aureus transposon which specifies resistances to erythromycin and spectinomycin, displays an unusually high degree of insertion specificity. Tn554 transposes with high efficiency to a unique ('primary') site in the S. aureus chromosome and only rarely (less than 10(-6) per transductant) to other, secondary sites. We report here the nucleotide sequences surrounding the junctions of Tn554 in three independent 'primary' insertions and two 'secondary' insertions of the transposon. Two unusual features are revealed: first, the termini of Tn554 contain neither inverted nor directly repeated sequences. Second, transposition of Tn554 does not generate the short direct repeats of the target DNA that are characteristic of other transposable elements. These results suggest that the mechanism of Tn554 insertion may be significantly different from that of other transposons.     

Hinf family: a novel repeated DNA family of the human genome

The isolation of a mutant adenovirus carrying an insertion of cellular DNA has led to the identification of a new family of human repetitive sequences, which are found tandemly arranged in the genome. The sequence of the viral insert resembles that of eukaryotic transposable elements.     

Apparent absence of transposable elements related to the P elements of D. melanogaster in other species of Drosophila

P elements are transposable elements found in P strain, but usually not in M strain, Drosophila melanogaster, and are responsible for the hybrid dysgenesis that occurs when male D. melanogaster of the P strain mate with females of the M strain (ref. 1 and references therein). Several P elements, which vary in length and genetic effects, have now been cloned. To investigate the evolutionary origin of P elements, we have used a cloned copy of a D. melanogaster P element to look for related sequences in the genomes of six other Drosophila species. We report here that, unlike many other transposable elements found in D. melanogaster, which seem also to be present in other Drosophila species, we have found no sequences closely enough related to P elements to be detected by DNA hybridization in any other Drosophila species. This result supports the hypothesis that P elements have recently invaded D. melanogaster by horizontal transmission.     

Activation of a transposable element in the germ line but not the soma of Caenorhabditis elegans

The genetic activity of transposable elements is tightly controlled in many species. Transposons that are relatively quiescent under certain circumstances can excise or transpose at greatly increased rates under other circumstances. For example, 'genomic shock' can activate quiescent maize transposons, 'cytotype' and tissue-specific splicing regulate Drosophila P factors, copy number controls Tn5 transposition in bacteria, and developmental timing affects the production of transposon-like intracisternal A-particles in mouse embryos. The Caenorhabditis elegans transposable element Tc1 is subject to both strain-specific and tissue-specific control. Multiple copies of Tc1 are present in the genome of all C. elegans strains collected from nature. However, these elements are genetically active in only certain isolates. For example, in C. elegans variety Bristol transposition and excision of Tc1 are undetectable, but in variety Bergerac transposition and excision are frequent. Moreover, in variety Bergerac, Tc1 is about 1,000-fold more active in somatic cells than in germ cells. We have investigated the genetic basis for the germ/soma regulation of Tc1 activity. We have isolated mutants that exhibit increased frequencies of Tc1 excision in the germ line. The frequencies of Tc1 excision in the soma are unaltered in these mutants. These mutants also exhibit high frequencies of Tc1 germ-line transposition, and this results in a mutator phenotype. Nearly all mutator-induced mutations are caused by insertion of Tc1.     

P-M hybrid dysgenesis does not mobilize other transposable element families in D. melanogaster

Mobilization of the P family of transposable elements in Drosophila melanogaster occurs in the hybrid progeny of males from an element-bearing strain (P strain) and females from an element-free strain (M strain). We tested whether the same crosses could mobilize other families of transposable elements. A mating scheme was used in which a set of X chromosomes was kept for 20 generations in either the active condition (known as hybrid dysgenesis) or the inactive condition (nondysgenic). Examination of 19 families of transposable elements by in situ hybridization indicated that only the P family was measurably mobilized under dysgenic conditions. Thus, P-M hybrid dysgenesis does not increase the transpositional activity of other families of transposable elements in D. melanogaster. We discuss possible explanations for several published reports to the contrary.     

A copia-like transposable element family in Arabidopsis thaliana

The fast generation time, small genome size and extensive genetic map of the crucifer Arabidopsis thaliana have made it the subject of an increasing number of studies in plant molecular genetics. As transposable elements have greatly facilitated genetic analysis in a variety of species, we have attempted to identify an endogenous A. thaliana transposable element. We report here the discovery of a family of such elements, which we refer to as Ta1 elements. Sequence analysis of one such element shows that it is closely related to retrotransposons and integrated retroviral proviruses, being bound by a direct sequence repeat and having an open reading frame with clear sequence similarity to the polyprotein of the Drosophila melanogaster retrotransposon copia. The sequence of an empty target site of a Ta1 element shows that insertion is accompanied by a five-base-pair target-site duplication and that Ta1 has transposed in the period of time since divergence of two races of A. thaliana.     

Role of transposable elements in heterochromatin and epigenetic control

Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.     

Insertion of the eukaryotic transposable element Ty1 creates a 5-base pair duplication

The his4-912 mutation results from insertion of a transposable element into the 5'-non-coding region of the his4 gene of yeast. A duplication of 5 base pairs of wild-type his4 DNA flanks the inserted element. The major class of His+ revertants result from excision of most of the transposable element, leaving an inserted segment of 334 base pairs flanked by the 5-base pair repeats.     

Transposition of an antibiotic resistance element in mycobacteria

Bacterial resistance to antibiotics is often plasmid-mediated and the associated resistance genes encoded by transposable elements. Mycobacteria, including the human pathogens Mycobacterium tuberculosis and M. leprae, are resistant to many antibiotics, and their cell-surface structure is believed to be largely responsible for the wide range of resistance phenotypes. Antibiotic-resistance plasmids have so far not been implicated in resistance of mycobacteria to antibiotics. Nevertheless, antibiotic-modifying activities such as aminoglycoside acetyltransferases and phosphotransferases have been detected in fast-growing species. beta-lactamases have also been found in most fast- and slow-growing mycobacteria. To date no mycobacterial antibiotic-resistance genes have been isolated and characterized. We now report the isolation, cloning and sequencing of a genetic region responsible for resistance to sulphonamides in M. fortuitum. This region also contains an open reading frame homologous to one present in Tn1696 (member of the Tn21 family) which encodes a site-specific integrase. The mycobacterial resistance element is flanked by repeated sequences of 880 base pairs similar to the insertion elements of the IS6 family found in Gram+ and Gram- bacteria. The insertion element is shown to transpose to different sites in the chromosome of a related fast-growing species, M. smegmatis. The characterization of this element should permit transposon mutagenesis in the analysis of mycobacterial virulence and related problems.     

Similar level of polyteny in bands and interbands of Drosophila giant chromosomes

The giant polytene chromosomes of Drosophila melanogaster have long been of interest to the geneticist because of the visible map of the genome provided by their characteristic banding patterns. An issue in the understanding of the molecular basis of chromosome banding has been whether the chromosomal DNA is replicated to the same extent in bands and interbands. Although various suggestions have been put forward the point has remained controversial. We have isolated 315 kilobases (kb) of contiguous Drosophila genomic DNA which spans an interval of approximately 13 bands and interbands of the polytene chromosomes. We report here the measurement of the relative level of DNA replication in polytene chromosomes of 84 adjacent restriction fragments of our cloned DNA. We conclude that there are no significant differences in the level of polyteny within the large band and between bands and interbands of this region. This result supports the 'folded fibre' model of polytene chromosome organization, rather than models involving disproportionate replication along the banding pattern.     

Temporal and spatial changes in Ca2+ distribution during the programmed cell death of tracheary elements

The changes in Ca²⁺ distribution in the tracheary elements (TEs) of the pepper leaves were studied using the cytochemical method of potassium antimonate. At the early stage of TEs formation, the vacuole and the nucleus held large volume, and antimonate Ca²⁺ deposits were observed mainly in the intercellular space and the cell wall. As the thickening of secondary wall occurred, the vacuole, nucleus and other organelles began to rupture, concomitant with the increase of calcium deposits in the cytosol, showing the influx of Ca²⁺ into the cell. With the further rupture of cytoplasm and other organelles, the number of calcium deposits at the non-thickening cell wall increased, but declined at the thickening bands of the secondary wall. When the cytoplasmic contents disappeared completely, the level of Ca²⁺ decreased at the non-thickening wall, but by contrast, increased at the thickening bands of the secondary wall. These observations indicated that the dynamic changes in Ca²⁺ distribution spatially and temporarily might have a close correlation with its distinct roles played during the formation of the secondary walls.     

Dual innervation of spinal ganglion neurons on perineum and bladder

Experiments were performed on 13 Wister rats. Fastblus (FB) was injected into subcutaneous tissue in perineum area and nuclear yellow (NY) was injected into subserous lamina of the bladder wall, respectively. FB, NY and FB+ NY were mostly found in the spinal ganglions of L6, S1 ans S2 segments. The numbers of FB, NY and FB+ NY labeled cells were 146, 186 and 81, in a total of 463 labeled cells and their proportion was 40%. 51% and 9%, respectively. The result indicates that the spinal ganglion neurons dually innervate both the somatic and visceral tissues, and the convergence of somato-visceral sensory pathways might occur in the spinal ganglion cells.     

An active DNA transposon family in rice

The publication of draft sequences for the two subspecies of Oryza sativa (rice), japonica (cv. Nipponbare) and indica (cv. 93-11), provides a unique opportunity to study the dynamics of transposable elements in this important crop plant. Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element (MITE) from any organism. A sequence classified as a Tourist-like MITE of 430 base pairs, called miniature Ping (mPing), was present in about 70 copies in Nipponbare and in about 14 copies in 93-11. These mPing elements, which are all nearly identical, transpose actively in an indica cell-culture line. Database searches identified a family of related transposase-encoding elements (called Pong), which also transpose actively in the same cells. Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome. Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation.