scholarly journals Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 129-142 ◽  
Author(s):  
J L Jakubczak ◽  
M K Zenni ◽  
R C Woodruff ◽  
T H Eickbush
Keyword(s):  
Drosophila Melanogaster ◽  
Critical Role ◽  
Rrna Genes ◽  
Type I ◽  
28S Rrna ◽  
Retrotransposable Elements ◽  
Total Percentage ◽  
Length Polymorphisms ◽  
Restriction Sites ◽  
Nucleotide Divergence

Abstract R1 and R2 are distantly related non-long terminal repeat retrotransposable elements each of which inserts into a specific site in the 28S rRNA genes of most insects. We have analyzed aspects of R1 and R2 abundance and sequence variation in 27 geographical isolates of Drosophila melanogaster. The fraction of 28S rRNA genes containing these elements varied greatly between strains, 17-67% for R1 elements and 2-28% for R2 elements. The total percentage of the rDNA repeats inserted ranged from 32 to 77%. The fraction of the rDNA repeats that contained both of these elements suggested that R1 and R2 exhibit neither an inhibition of nor preference for insertion into a 28S gene already containing the other type of element. Based on the conservation of restriction sites in the elements of all strains, and sequence analysis of individual elements from three strains, nucleotide divergence is very low for R1 and R2 elements within or between strains (less than 0.6%). This sequence uniformity is the expected result of the forces of concerted evolution (unequal crossovers and gene conversion) which act on the rRNA genes themselves. Evidence for the role of retrotransposition in the turnover of R1 and R2 was obtained by using naturally occurring 5' length polymorphisms of the elements as markers for independent transposition events. The pattern of these different length 5' truncations of R1 and R2 was found to be diverse and unique to most strains analyzed. Because recombination can only, with time, amplify or eliminate those length variants already present, the diversity found in each strain suggests that retrotransposition has played a critical role in maintaining these elements in the rDNA repeats of D. melanogaster.

scholarly journals The cytogenetic boundaries of the rDNA region within heterochromatin of the X chromosome of Drosophila melanogaster and their relation to male meiotic pairing sites

1982 ◽  
Vol 39 (2) ◽  
pp. 149-156 ◽  
Author(s):  
R. Appels ◽  
A. J. Hilliker
Keyword(s):  
Drosophila Melanogaster ◽  
Rrna Genes ◽  
Type I ◽  
28S Rrna ◽  
Meiotic Pairing ◽  
Coding Region ◽  
Intervening Sequences ◽  
Single Region ◽  
Rrna Sequences

SummaryThe proximal breakpoints of the inversion chromosomes In(1)ωm4 and In(1)m51b were shown, by in situ hybridization, to define the boundaries of the ribosomal DNA region located within the X chromosome heterochromatin (Xh). We estimate that at least 95% of the rDNA is located between the In(1)ωm4 and In(1)ωm51b proximal breakpoints. In contrast only 60–70% of the Type I intervening sequences located in Xh are located between these breakpoints. The Type I intervening sequences in the rDNA region occur as inserts in the 28S rRNA sequences while the remainder of the sequences are distal to the In(1)ωm4 breakpoint and not associated with rRNA genes.The regions of Xh which contain rDNA and Type I intervening sequences were related to regions shown by Cooper (1964) to contribute to meiotic pairing between the X and Y chromosomes in male Drosophila. We demonstrate that the rRNA coding region contributes to X / Y pairing. However, no single region of Xh is required for fidelity of male meiotic pairing of the sex chromosomes.

scholarly journals Chromosomal distribution of the major insert in Drosophila melanogaster 28S rRNA genes

1981 ◽  
Vol 37 (2) ◽  
pp. 209-214 ◽  
Author(s):  
W. J. Peacock ◽  
R. Appels ◽  
S. Endow ◽  
D. Glover
Keyword(s):  
Drosophila Melanogaster ◽  
Polytene Chromosomes ◽  
Ribosomal Gene ◽  
Rrna Genes ◽  
Major Type ◽  
Type I ◽  
28S Rrna ◽  
Mitotic Chromosomes ◽  
Chromosomal Distribution

SUMMARYThe major type I insert sequence for the 28S rRNA genes of Drosophila melanogaster has been mapped within the chromosomes using a probe synthesized from a cloned sequence containing the entire 5·4 kb segment. The genomic distribution was shown to be complex in that the insert sequence occurred next to many different types of sequences, in addition to occurring as an insert in the 28S rRNA genes of the X chromosome. In situ hybridization of mitotic chromosomes showed most of the insert units not contained in the ribosomal genes to be located near the ribosomal gene cluster on the X chromosome. Additional sites were detected in polytene chromosomes in region 102C, 8–12 and in the hetero-chromatin of the autosomes.

Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster

1986 ◽  
Vol 6 (4) ◽  
pp. 1023-1031
Author(s):  
R Terracol ◽  
N Prud'homme
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Copy Number ◽  
Rdna Locus ◽  
Gene Copy ◽  
Specific Gene ◽  
Type I ◽  
28S Rrna ◽  
Wild Type ◽  
Y Chromosomes ◽  
Genes Encoding

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

scholarly journals Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster.

1986 ◽  
Vol 6 (4) ◽  
pp. 1023-1031 ◽  
Author(s):  
R Terracol ◽  
N Prud'homme
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Copy Number ◽  
Rdna Locus ◽  
Gene Copy ◽  
Specific Gene ◽  
Type I ◽  
28S Rrna ◽  
Wild Type ◽  
Y Chromosomes ◽  
Genes Encoding

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

scholarly journals Epigenetic Regulation of Retrotransposons within the Nucleolus of Drosophila

2008 ◽  
Vol 28 (20) ◽  
pp. 6452-6461 ◽  
Author(s):  
Danna G. Eickbush ◽  
Junqiang Ye ◽  
Xian Zhang ◽  
William D. Burke ◽  
Thomas H. Eickbush
Keyword(s):  
Large Scale ◽  
Transcriptional Control ◽  
Rdna Locus ◽  
Rrna Genes ◽  
28S Rrna ◽  
Nucleolar Dominance ◽  
Retrotransposable Elements ◽  
Active Line ◽  
Interspecies Hybrids ◽  
Rdna Loci

ABSTRACT R2 retrotransposable elements exclusively insert into a conserved region of the tandemly organized 28S rRNA genes. Despite inactivating a subset of these genes, R2 elements have persisted in the ribosomal DNA (rDNA) loci of insects for hundreds of millions of years. Controlling R2 proliferation was addressed in this study using lines of Drosophila simulans previously shown to have either active or inactive R2 retrotransposition. Lines with active retrotransposition were shown to have high R2 transcript levels, which nuclear run-on transcription experiments revealed were due to increased transcription of R2-inserted genes. Crosses between R2 active and inactive lines indicated that an important component of this transcriptional control is linked to or near the rDNA locus, with the R2 transcription level of the inactive parent being dominant. Pulsed-field gel analysis suggested that the R2 active and inactive states were determined by R2 distribution within the locus. Molecular and cytological analyses further suggested that the entire rDNA locus from the active line can be silenced in favor of the locus from the inactive line. This silencing of entire rDNA loci represents an example of the large-scale epigenetic control of transposable elements and shares features with the nucleolar dominance frequently seen in interspecies hybrids.

scholarly journals Integration of Bombyx mori R2 Sequences into the 28S Ribosomal RNA Genes of Drosophila melanogaster

2000 ◽  
Vol 20 (1) ◽  
pp. 213-223 ◽  
Author(s):  
Danna G. Eickbush ◽  
Dongmei D. Luan ◽  
Thomas H. Eickbush
Keyword(s):  
Drosophila Melanogaster ◽  
Bombyx Mori ◽  
Dna Sequences ◽  
Reverse Transcription ◽  
Rrna Genes ◽  
Hydroxyl Group ◽  
28S Rrna ◽  
Gene Sequences ◽  
Gene Target ◽  
Integration System

ABSTRACT R2 non-long-terminal-repeat retrotransposable elements integrate into a precise location in the 28S rRNA genes of arthropods. The purified protein encoded by R2 can cleave the 28S gene target site and use the 3′ hydroxyl group generated by this cleavage to prime reverse transcription of its own RNA, a process called target-primed reverse transcription. An integration system is described here in which components from the R2 element of the silkmoth, Bombyx mori, are injected into the preblastoderm embryo ofDrosophila melanogaster. Silkmoth R2 sequences were readily detected in the 28S rRNA genes of the surviving adults as well as in the genes of their progeny. The 3′ junctions of these insertions were similar to those seen in our in vitro assays, as well as those from endogenous R2 retrotransposition events. The 5′ junctions of the insertions originally contained major deletions of both R2 and 28S gene sequences, a problem overcome by the inclusion of upstream 28S gene sequences at the 5′ end of the injected RNA. The resulting 5′ junctions suggested a recombination event between the cDNA and the upstream target sequences. This in vivo integration system should help determine the mechanism of R2 retrotransposition and be useful as a delivery system to integrate defined DNA sequences into the rRNA genes of organisms.

scholarly journals Retrotransposable Elements R1 and R2 in the rDNA Units of Drosophila mercatorum: abnormal abdomen Revisited

Genetics ◽  
1999 ◽  
Vol 151 (2) ◽  
pp. 653-665 ◽  
Author(s):  
Harmit S Malik ◽  
Thomas H Eickbush
Keyword(s):  
Population Level ◽  
Selective Advantage ◽  
Rrna Genes ◽  
Level Shift ◽  
28S Rrna ◽  
Rdna Unit ◽  
Retrotransposable Elements ◽  
Drosophila Mercatorum ◽  
Younger Age ◽  
Type Strains

Abstract R1 and R2 retrotransposable elements are stable components of the 28S rRNA genes of arthropods. While each retrotransposition event leads to incremental losses of rDNA unit expression, little is known about the selective consequences of these elements on the host genome. Previous reports suggested that in the abnormal abdomen (aa) phenotype of Drosophila mercatorum, high levels of rDNA insertions (R1) in conjunction with the under-replication locus (ur), enable the utilization of different ecological conditions via a population level shift to younger age. We have sequenced the R1 and R2 elements of D. mercatorum and show that the levels of R1- and R2-inserted rDNA units were inaccurately scored in the original studies of aa, leading to several misinterpretations. In particular, contrary to earlier reports, aa flies differentially underreplicate R1- and R2-inserted rDNA units, like other species of Drosophila. However, aa flies do not undergo the lower level of underreplication of their functional rDNA units (general underreplication) that is seen in wild-type strains. The lack of general underreplication is expected to confer a selective advantage and, thus, can be interpreted as an adaptation to overcome high levels of R1 and R2 insertions. These results allow us to reconcile some of the apparently contradictory effects of aa and the bobbed phenotype found in other species of Drosophila.

scholarly journals Characterization of ribosomal DNA (rDNA) in Drosophila arizonae

2000 ◽  
Vol 23 (2) ◽  
pp. 231-233
Author(s):  
Francisco Javier Tovar ◽  
Luiz Antônio Ferreira da Silva ◽  
Renato Santos Rodarte ◽  
Orilio Leoncini
Keyword(s):  
Ribosomal Dna ◽  
Rrna Genes ◽  
Regulatory Sequences ◽  
28S Rrna ◽  
Retrotransposable Element ◽  
Repleta Group ◽  
Drosophila Arizonae ◽  
Restriction Sites ◽  
Multigenic Family

Ribosomal DNA (rDNA) is a multigenic family composed of one or more clusters of repeating units (RU). Each unit consists of highly conserved sequences codifying 18S, 5.8S and 28S rRNA genes intercalated with poorly conserved regulatory sequences between species. In this work, we analyzed the rDNA of Drosophila arizonae, a member of the mulleri complex (Repleta group). Using genomic restriction patterns, cloning and mapping of some representative rDNA fragments, we were able to construct a representative restriction map. RU in this species are 13.5-14 kb long, restriction sites are completely conserved compared with other drosophilids and the rDNA has an R1 retrotransposable element in some RU. We were unable to detect R2 elements in this species.

Rates of R1 and R2 Retrotransposition and Elimination From the rDNA Locus of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 799-811 ◽  
Author(s):  
César E Pérez-González ◽  
Thomas H Eickbush
Keyword(s):  
Drosophila Melanogaster ◽  
Concerted Evolution ◽  
Inbred Lines ◽  
Rdna Locus ◽  
Mobile Elements ◽  
Rrna Genes ◽  
28S Rrna ◽  
Ltr Retrotransposons ◽  
A Genome ◽  
Rdna Loci

Abstract R1 and R2 elements are non-LTR retrotransposons that insert specifically into the 28S rRNA genes of arthropods. The process of concerted evolution of the rDNA locus should give rise to rapid turnover of these mobile elements compared to elements that insert at sites throughout a genome. To estimate the rate of R1 and R2 turnover we have examined the insertion of new elements and elimination of old elements in the Harwich mutation accumulation lines of Drosophila melanogaster, a set of inbred lines maintained for >350 generations. Nearly 300 new insertion and elimination events were observed in the 19 Harwich lines. The retrotransposition rate for R1 was 18 times higher than the retrotransposition rate for R2. Both rates were within the range previously found for retrotransposons that insert outside the rDNA loci in D. melanogaster. The elimination rates of R1 and R2 from the rDNA locus were similar to each other but over two orders of magnitude higher than that found for other retrotransposons. The high rates of R1 and R2 elimination from the rDNA locus confirm that these elements must maintain relatively high rates of retrotransposition to ensure their continued presence in this locus.

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