Rates of movement of transposable elements on the second 
chromosome of Drosophila melanogaster

The rates of movement of 11 families of transposable elements of Drosophila melanogaster were studied by means of in situ hybridization of probes to polytene chromosomes of larvae from a long-term mutation accumulation experiment. Replicate mutation-accumulation lines carrying second chromosomes derived from a single common ancestral chromosome were maintained by backcrosses of single males heterozygous for a balancer chromosome and a wild-type chromosome, and were scored after 116 generations. Twenty-seven transpositions and 1 excision were detected using homozygous viable and fertile second chromosomes, for a total of 235056 potential sources of transposition events and a potential 252880 excision events. The overall transposition rate per element per generation was 1·15×10−4 and the excision rate was 3·95×10−6. The single excision (of a roo element) was due to recombination between the element's long terminal repeats. A survey of the five most active elements among nine homozygous lethal lines revealed no significant difference in the estimates of transposition and excision rates from those from viable lines. The excess of transposition over excision events is in agreement with the results of other in situ hybridization experiments, and supports the conclusion that replicative increase in transposable element copy number is opposed by selection. These conclusions are compared with those from other studies, and with the conclusions from population surveys of element frequencies.

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Long-term evolution of the roo transposable element copy number in mutation accumulation lines of Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672311000103 ◽

2011 ◽

Vol 93 (3) ◽

pp. 181-187 ◽

Cited By ~ 7

Author(s):

JULIA DÍAZ-GONZÁLEZ ◽

J. FERNANDO VÁZQUEZ ◽

JESÚS ALBORNOZ ◽

ANA DOMÍNGUEZ

Keyword(s):

Drosophila Melanogaster ◽

De Novo ◽

Accumulation Rate ◽

Mutation Accumulation ◽

Fundamental Parameter ◽

Highly Active ◽

Transposition Rate ◽

Transposable Element Copy

SummaryThe rate of insertion of transposable elements (TEs) is a fundamental parameter to understand both their dynamics and role in the evolution of the eukaryotic genome. Nonetheless, direct estimates of insertion rates are scarce because transposition is in general a rare phenomenon. A great deal of our previous work on transposition was based on a set of long-term mutation accumulation (MA) lines of Drosophila melanogaster started in 1987 (Oviedo lines), where roo was found highly active, with a rate of insertion of 7×10−4 insertions per element and generation, as compared with other 15 TE families that presented transposition rates around 10−5. Here, we study the evolution of the roo transposition rate, by in situ hybridization, after 60–75 additional generations of MA in two subsets of the Oviedo lines, O and O′, which had achieved average numbers of roo insertions of 77 and 84, respectively. In the O lines, insertions accumulated at a rate that remained constant (7×10−4 insertions per element and generation); however, the subset of lines O′ showed a lower accumulation rate of 4×10−4 insertions per element per generation, suggesting a regulation of transposition that depends on the number of elements. However, one of the O′ lines reached a number of 103 insertions, departing from the group mean by 4·6 sd, and showing that it escapes regulation. Hence, ‘de novo’ mutations affecting the regulation of transposition are relatively common. These results are discussed in relation to the possible mechanisms of containment of TEs.

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The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution

Genetics Research ◽

10.1017/s0016672300030792 ◽

1992 ◽

Vol 60 (2) ◽

pp. 103-114 ◽

Cited By ~ 65

Author(s):

Brian Charlesworth ◽

Angela Lapid ◽

Darlene Canada

Keyword(s):

Population Dynamics ◽

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Transposable Elements ◽

Copy Number ◽

Polytene Chromosomes ◽

Chromosome Band ◽

High Frequencies ◽

Copy Numbers

SummaryData were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. 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 data suggest that the rate of transposition perelement per generation is of the order of 10−4, for the elements included in this study.

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

Genetics Research ◽

10.1017/s0016672300028482 ◽

1989 ◽

Vol 54 (2) ◽

pp. 113-125 ◽

Cited By ~ 39

Author(s):

Brian Charlesworth ◽

Angela Lapid

Keyword(s):

Drosophila Melanogaster ◽

Transposable Elements ◽

Copy Number ◽

Distal Part ◽

Polytene Chromosomes ◽

Chromosome Band ◽

X Chromosomes ◽

High Frequencies ◽

Chromosome Element

SummaryData 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.

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Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs Southern blotting data

Genetics Research ◽

10.1017/s0016672301005201 ◽

2001 ◽

Vol 78 (2) ◽

pp. 121-136 ◽

Cited By ~ 44

Author(s):

XULIO MASIDE ◽

CAROLINA BARTOLOMÉ ◽

STAVROULA ASSIMACOPOULOS ◽

BRIAN CHARLESWORTH

Keyword(s):

Drosophila Melanogaster ◽

Transposable Elements ◽

Southern Blotting ◽

Polytene Chromosomes ◽

Element Abundance ◽

Data Sets ◽

Copy Numbers ◽

Blotting Technique ◽

Controlling Element

Genomic copy numbers and the rates of movement of nine families of transposable elements (TEs) of Drosophila melanogaster were estimated in two sets of mutation accumulation lines: Beltsville and Madrid. Southern blotting was used to screen a large number of samples from both genetic backgrounds for TEs. The Madrid lines were also screened by in situ hybridization of TEs to polytene chromosomes, in order to obtain more detailed information about the behaviour of TEs in the euchromatin. Southern blotting data provided evidence of insertions and excision events in both genetic backgrounds, occurring at rates of approximately 10−5 and 10−6 per element copy per generation, respectively. In contrast, in situ data from the Madrid background presented a completely different picture, with no evidence for excisions, and a significantly higher rate of transposition (1·01×10−4). Direct comparison of the two data sets suggests that the Southern blotting technique had serious deficiencies: (i) it underestimated element abundance; (ii) it revealed less than 30% of the new insertions detected by in situ hybridization; and (iii) changes in the size of restriction fragments from any source were spuriously identified as simultaneous insertion–excision events. Our in situ data are consistent with previous studies, and suggest that selection is the main force controlling element spread by transposition.

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The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. II. Inferences on the nature of selection against elements

Genetics Research ◽

10.1017/s0016672300030809 ◽

1992 ◽

Vol 60 (2) ◽

pp. 115-130 ◽

Cited By ~ 60

Author(s):

Brian Charlesworth ◽

Angela Lapid ◽

Darlene Canada

Keyword(s):

Drosophila Melanogaster ◽

Transposable Elements ◽

Polytene Chromosomes ◽

Element Abundance ◽

General Tendency ◽

Fourth Chromosome ◽

Considerable Heterogeneity ◽

Fitness Consequences ◽

Random Expectation

SummaryData were collected on the distribution of nine families of transposable elements among a sample of autosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of biotinylated probes to polytene chromosomes. There is no general tendency for elements to accumulate at the tips of chromosomes. Elements tend to be present in excess of random expectation in the euchromatin proximal to the centromeres of the major autosomes, and on chromosome four. There is considerable heterogeneity between different families in the extent of this excess. The overall abundance of element families is inversely related to the extent to which they accumulate proximally. The level of proximal accumulation for the major autosomes is similar to that on the fourth chromosome, but less than that for the X chromosome. There is an overall deficiency of elements in the mid-section of the X compared with the mid-sections of the major autosomes, with considerable heterogeneity between families. The magnitude of this deficiency is positively related to the extent to which elements accumulate proximally. No such deficiency is seen if the proximal regions of the X and autosomes are compared. There is a small and non-significant excess of elements in third chromosomes carrying inversions. There is some between-year heterogeneity in element abundance. The implications of these findings are discussed, and it is concluded that they generally support the hypothesis that transposable element abundance is regulated primarily by the deleterious fitness consequences of meiotic ectopic exchange between elements. If this is the case, such exchange must be very infrequent in the proximal euchromatin, and the elements detected in population surveys of this kind must be inserted into sites where they have negligible mutational effects on fitness.

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

Genetics Research ◽

10.1017/s0016672300032845 ◽

1994 ◽

Vol 64 (3) ◽

pp. 183-197 ◽

Cited By ~ 54

Author(s):

Brian Charlesworth ◽

Philippe Jarne ◽

Stavroula Assimacopoulos

Keyword(s):

Drosophila Melanogaster ◽

Transposable Elements ◽

Natural Population ◽

Polytene Chromosomes ◽

Control Element ◽

Element Abundances ◽

Evolutionary Forces ◽

Isogenic Lines ◽

Copy Numbers

SummaryThe 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 β-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.

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Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number

Genetics ◽

10.1093/genetics/144.1.197 ◽

1996 ◽

Vol 144 (1) ◽

pp. 197-204

Author(s):

Christine Hoogland ◽

Christian Biémont

Keyword(s):

Drosophila Melanogaster ◽

Transposable Elements ◽

Dna Content ◽

Recombination Rate ◽

Alternative Hypothesis ◽

Insertion Site ◽

Polytene Chromosomes ◽

Negative Relationship ◽

Site Occupancy ◽

Site Number

Abstract Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.

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Permacol Collagen Paste Injection for Treatment of Complex Cryptoglandular Anal Fistulas: An Observational Cohort Study With a 2-Year Follow-up

Surgical Innovation ◽

10.1177/1553350618808120 ◽

2018 ◽

Vol 26 (2) ◽

pp. 168-179 ◽

Cited By ~ 3

Author(s):

Michele Schiano di Visconte ◽

Andrea Braini ◽

Luana Moras ◽

Luigi Brusciano ◽

Ludovico Docimo ◽

...

Keyword(s):

Anal Fistulas ◽

Recurrent Fistula ◽

Pain Scores ◽

Significant Difference ◽

Paste Extrusion ◽

Observational Cohort ◽

Grading Scale

Background. Permacol paste injection is a novel treatment approach for complex cryptoglandular anal fistulas. This study was performed to evaluate the long-term clinical outcomes of treatment with Permacol paste for complex cryptoglandular fistulas. Methods. Patients with primary or recurrent complex cryptoglandular anal fistulas treated with Permacol paste from 2014 to 2016 were retrospectively analyzed. Results. A total of 46 patients (median age, 41.3 years; 21 female) underwent Permacol paste injection; 20 patients (43%) had previously undergone failed fistula surgery. The patients had experienced anal fistula-related symptoms for a median of 10 weeks (range, 3-50 weeks). All patients had a draining seton in situ for a median of 10 weeks (range, 4-46 weeks). The median follow-up time was 24 months (range, 1-25 months). At the 1-month follow-up, 2 patients had paste extrusion and 2 had anal abscesses. The mean preoperative Continence Grading Scale score was 1.10 ± 1.40, and that at 3 months postoperatively was 1.13 ± 1.39 ( P = .322). There was a significant difference in the preoperative and the 1- and 3-month postoperative pain scores ( P < .001). At the 24-month follow-up, the healing rate was 50% (n = 23). A total of 19 patients (41%) with a recurrent fistula after failed Permacol paste injection required additional operative procedures. The satisfaction rate at the 2-year follow-up was 65%. Conclusion. Permacol paste injection is minimally invasive and technically easy to perform. It can be considered as a viable and reasonable option for the treatment of complex cryptoglandular anal fistulas in patients with fecal continence disorders.

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Quantitative in situ hybridization of ribosomal RNA species to polytene chromosomes of Drosophila melanogaster

Journal of Molecular Biology ◽

10.1016/0022-2836(77)90170-x ◽

1977 ◽

Vol 115 (3) ◽

pp. 539-563 ◽

Cited By ~ 74

Author(s):

Paul Szabo ◽

Robert Elder ◽

Dale M. Steffensen ◽

Olke C. Uhlenbeck

Keyword(s):

Drosophila Melanogaster ◽

In Situ Hybridization ◽

Ribosomal Rna ◽

Polytene Chromosomes

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Transmission pattern of hobo transposable element in transgenic lines of Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672398003127 ◽

1998 ◽

Vol 71 (2) ◽

pp. 97-107 ◽

Cited By ~ 13

Author(s):

VERONIQUE LADEVEZE ◽

IBO GALINDO ◽

NICOLE CHAMINADE ◽

LUIS PASCUAL ◽

GEORGES PERIQUET ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Population Studies ◽

Insertion Site ◽

Molecular Analyses ◽

Transgenic Lines ◽

Genomic Dnas ◽

Insertion Sites ◽

Method Show

This study is an attempt to trace the fate of hobo elements in the genomes of E strains of Drosophila melanogaster that have been transfected with pHFL1, a plasmid containing an autonomous hobo. Such long-term population studies (over 105 generations) could be very useful for better understanding the population and genomic dynamics of transposable elements and their pattern of insertions. Molecular analyses of hobo elements in the transfected lines were performed using Southern blots of XhoI-digested genomic DNAs. The complete element was observed in all six injected lines. In two lines we observed, at generation 100, two deleted elements, which did not correspond to Th1 and Th2. The results obtained by the in situ method show that the number of hybridization sites increases in each line and prove that the hobo element may be amplified in an RM genome. The hobo activity does not seem to be systematically correlated with the number of hobo elements. After generation 85, the evolution of the hobo element's insertion site number depends on the injected line. In all lines, the total number of insertions remains quite small, between 0 and 11. Hobo elements are located on each of the chromosomal arms. We describe ‘hotspots’ – insertion sites present in all lines and in all generations. On the 3R arm, a short inversion appeared once at generation 85.

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