Two distinct intervening sequences in different ribosomal DNA repeat units of Sciara coprophila

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.

Molecular and cytological characterization of repetitive DNA sequences from the centromeric heterochromatin of Sciara coprophila

Sciara coprophila (Diptera, Nematocera) constitutes a classic model to analyze unusual chromosome behavior such as the somatic elimination of paternal X chromosomes, the elimination of the whole paternal, plus non-disjunction of the maternal X chromosome at male meiosis. The molecular organization of the heterochromatin in S. coprophila is mostly unknown except for the ribosomal DNA located in the X chromosome pericentromeric heterochromatin. The characterization of the centromeric regions, thus, is an essential and required step for the establishment of S. coprophila as a model system to study fundamental mechanisms of chromosome segregation. To accomplish such a study, heterochromatic sections of the X chromosome centromeric region from salivary glands polytene chromosomes were microdissected and microcloned. Here, we report the identification and characterization of two tandem repeated DNA sequences from the pericentromeric region of the X chromosome, a pericentromeric RTE element and an AT-rich centromeric satellite. These sequences will be important tools for the cloning of S. coprophila centromeric heterochromatin using libraries of large genomic clones.

Structural constraints in expansion segments from a midge 26S rDNA

DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displayed a local bias in nucleotide composition toward AT. These regions were identified as expansion segments D3, D4, D5, D6, D7a, and D12. Besides base sequence divergence, differences in length were observed between the respective variable domains of the two species, particularly for D7a. Prediction of secondary structure showed that the folding of the Chironomus expansion segments analyzed is in agreement with the general patterns proposed for eukaryotic LSU rRNA. The comparison with Drosophila revealed also that the Chironomus secondary structures of the variable domains are supported by multiple compensatory substitutions or even compensatory insertions. Chironomus D7a displayed an unusual structural feature with respect to the insect D7a models that have been inferred up to now. The structural constraint observed in the expansion segments of Diptera so distantly related as midges and Drosophila suggests that these regions contribute to some functional role. Concerning the D7a of insects so far analyzed, there can be, in addition to a conserved secondary structure, a nucleotide composition constraint that might be important for the process giving rise to the alpha and beta halves of the 26S rRNA.

Characterization of Aphidius ervi (Hymenoptera, Braconidae) ribosomal genes and identification of site-specific insertion elements belonging to the non-LTR retrotransposon family

We performed a molecular analysis of the Aphidius ervi ribosomal gene structure. This insect belongs to a set of closely related Aphidiinae species of the genus Aphidius Nees, of relevant interest in biological control. We constructed A. ervi genomic libraries, cloned and characterized several rDNA repeating units and sequenced different regions of the rDNA cistrons. We have found that insertion sequences interrupt the A. ervi 28S rDNA genes: the sequences of the two 5' and 3' insertion-28S junctions show that the elements are present at the position where R1 elements have been found in various insect species. In addition, the insertion of the element produces a duplication of the 14 nt target region. The sequence analysis indicates that the A. ervi elements belong to the R1 retrotransposon family with a highly conserved reverse transcriptase domain.

The ribosomal genes of the mosquito, Aedes aegypti

The characterisation of the ribosomal genes of the mosquito, Aedes aegypti, is described. Preliminary experiments using a cloned Drosophila ribosomal DNA (rDNA) repeat to probe Southern transfers of Ae. aegypti genomic DNA has indicated that the rDNA repeat of Ae. aegypti is 9.0 kb in length and that individual rDNA repeats exhibit a high degree of homogeneity with respect to length and the position of restriction enzyme recognition sites within the rDNA. The preliminary mapping data together with partial digestion experiments demonstrate that, as in all other higher eukaryotes, the rDNA repeats are arranged in a head-to-tail, tandemly repeating manner. The restriction mapping of cloned rDNA repeats confirmed the largely uniform length of the Ae. aegypti rDNA repeat and provided a more detailed physical map of the DNA. A restriction site polymorphism was detected in one clone (Aar9) which contains an extra HincII site, which is not present in three other clones studied (Aar1, Aar3, or Aar7). Transcription mapping has allowed the allocation of identities to the various restriction fragments and the approximate positioning of the transcription unit. The estimate of rDNA repeat copy number in Ae. aegypti (approximately 500 copies per haploid genome) is similar to the estimate reported for the closely related species, Aedes albopictus, of 430 copies per haploid genome. Ribosomal DNA thus comprises approximately 0.6% of the total Ae. aegypti genome. Analysis of the variation of the rDNA repeat unit both within individual mosquitoes and between strains of Ae. aegypti, has severed to confirm the remarkable homogeneity of the rDNA repeat unit in this insect.

Isolation and characterization of ribosomal DNA variants from Sciara coprophila

The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer length variants in Sciara, we found a variant due to the insertion of a putative mobile element (lambda Bc11), and variants containing ribosomal insertion elements. By DNA sequence analysis of rDNA/non-rDNA junctions, there are three distinct types of ribosomal insertion elements found in Sciara rDNA: two correspond to the R1 and R2 insertion elements found in other dipterans (clones lambda Bc5 and pBc1L1, respectively), and one is a novel class of ribosomal insertion elements (R3, exemplified by clone pBc6D6) which so far is unique to Sciara. Together, the several different rDNA variants make up from 12 to 20% of the rDNA in Sciara. These results are discussed in the context of evolution of the ribosomal RNA multigene family.

Tsetse fly rDNA: an analysis of structure and sequence

A genomic library of Glossina morsitans morsitans (tsetse fly) has been constructed in the phage vector EMBL 4 and a complete rDNA unit isolated by using a D. melanogaster rDNA clone as a probe. The overall organisation is typical of higher eukaryotes, including an intergenic spacer consisting of a subrepeating structure. Atypically, however, the 45S precursor RNA promoter was shown to lie within the last subrepeat by S1 mapping; i.e. the last subrepeat extends 90 bp into the ETS. The sequence of the spacer subrepeats, the ETS and the first 151 nucleotides of the 18S gene was determined. Comparisons with the corresponding regions of other higher eukaryotes, including insects shows that the ETS has completely diverged, raising questions concerning their functional significance and evolutionary retention; depending on the method of alignment, only two short regions of reasonable homology are shared with Drosophila species: a stretch of nucleotides around the transcription initiation site, and AACATA at the NTS-18S gene junction; and the functionally important G at -16, conserved in all other examined species, is displaced no matter what method of alignment is used. These and other features reflect continual processes of change in the rDNA family to which the several functions of the repeating unit need to adjust.

rRNA processing: removal of only nineteen bases at the gap between 28S alpha and 28S beta rRNAs in Sciara coprophila

We have determined the sequence of the rDNA region between the 28S alpha and 28S beta rRNA coding segments (termed a "gap") in the insect Sciara coprophila, and have used S1 nuclease mapping and cDNA primer extension to define the 5' and 3' boundaries of the gap. Only 19 bases found in rDNA at the gap region are absent from mature 28S rRNA. Eukaryotic rRNAs contain stretches of nucleotides ("expansion segments") which are absent in E. coli rRNA. The gap region in Sciara is located within expansion segment V. Therefore, the excision of 19 bases in the Sciara gap suggests that a large portion of expansion segment V plays no function in mature ribosomes. Specific sequences conserved in Sciara and Drosophila are considered as candidates for recognition signals for the excision of the gap transcript.

rDNA in Locusta migratoria is very variable: two introns and extensive restriction site polymorphisms in the spacer

Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two introns of different length were found at different positions in the 28S gene. They are present in less than 5% of the genes.

Ribosomal DNA genes of Bombyx mori: a minor fraction of the repeating units contain insertions

We have analyzed multiple recombinant DNA clones containing ribosomal RNA repeat units of the silkmoth, Bombyx mori. In combination with genomic DNA blots, analysis of these clones indicated that the rDNA repeat of B. mori is 10.8 kilobase pair in length and tandemly repeated in the genome, as reported by Manning et al. (18). However, contrary to that report, approximately 12% of the rDNA cistrons are interrupted by insertions of non-ribosomal DNA. Two classes of DNA insertions were identified. In one class the insertions are positioned in a region of the 28S coding sequence similar to that of the predominant rDNA insertions found in a variety of Dipteran and Tetrahymena species. In the second class, probable insertions are found close to the 3' terminus of the 28S coding sequence. Restriction enzyme analysis indicates that the two classes of insertions are not related.

The intron boundaries and flanking rRNA coding sequences of Calliphora erythrocephala rDNA

We have sequenced the available cloned examples of the intron-coding sequence junctions for the rDNA of the higher Dipteran, Calliphora erythrocephala. The introns interrupt the rDNA at the same position as the type 1 intron family detected in Drosophila melanogaster and D. virilis (10,11). A duplication of 14 base pairs of the 28S rRNA coding sequence surrounds a short version of the major genomic length class of introns. This same duplication is associated with boundaries of the type 1 introns in D. virilis and D. melanogaster (10, 13,14). We have detected considerable homology between the 3' intron sequences of C. erythrocephala and D. virilis. The rRNA coding sequences flanking the introns are extremely homologous in C. erythrocephala, D. melanogaster and D. virilis, with only one small region of significant divergence. This corresponds to a variable stem region previously identified in eukaryotic 28S rRNA at a site analogous to the L1 ribosomal protein binding site of prokaryotic 23S rRNA (27).

Structural organization of the two main rDNA size classes of Ascaris lumbricoides

The two main rDNA size classes in the genome of Ascaris lumbricoides consist of 8.8 kb and 8.4 kb long repeating units present in a quantitative ratio of roughly 10:1. They both contain the genes coding for 18 , 5.8S and 26S ribosomal RNAs. The length heterogeneity is due to a 450 bp long spacer region localized in the longer repeating unit which begins 870 bp upstream of the 5'-end 18S gene. A few additional microheterogeneities in base sequence occur at the 5'-end of the 26S gene. The 18S, 5.8S and 26S coding regions have been mapped on both the 8.8 kb and 8.4 kb repeating units and the localization of the 5'- and 3'-ends of the 18S and 26S genes has been performed by S1 protection. No intervening sequences are present in either coding region of the two main rDNA size classes.

Cloning and analysis of ribosomal DNA of Chironomus thummi piger and Chironomus thummi thummi. The nontranscribed spacer of Ch. th. thummi contains a highly repetitive DNA sequence

The ribosomal DNAs from Ch. thummi piger and Ch. th. thummi were cloned and analysed by a variety of restriction endonucleases. Comparison of rDNA clones from the two subspecies revealed a considerable length difference: the length of the analysed rDNA cistrons is approximately 9.0 kb for Ch. th. piger and approximately 14.5 kb for Ch. th. thummi. The nearly 5 kb additional DNA in Ch. th. thummi is clearly located within the non-transcribed spacer region, and consists of AT-rich, repetitive DNA elements. These elements with a basic repeat length of approximately 120 bp, are arranged tandemly in stretches of up to about 50 identical copies, which are characterized by a cleavage site for ClaI restriction endonuclease. They are found only in the Ch. th. thummi rDNA clones and not in the Ch. th. piger clones. Southern hybridizations between cloned ribosomal DNA and "centromeric" highly repetitive DNA have shown that the ribosomal repetitive Cla-elements are closely related to a highly repetitive DNA sequence family, which is present in various chromosomal sites particularly the centromeres. Sequence analysis has revealed more than 90% homology between the ribosomal Cla-elements and the "centromeric" Cla-elements.--Since it is clear from cytological investigations that Ch. th. piger with the small rDNA repeating unit is the phylogenetically older subspecies, we postulate a transposition of Cla-elements into the nucleolar DNA during the evolution of Ch. th. thummi.

Duplicated rDNA sequences of variable lengths flanking the short type I insertions in the rDNA of Drosophila melanogaster

We describe cloned segments of rDNA that contain short type I insertions of differing lengths. These insertions represent a coterminal subset of sequences from the right hand side of the major 5kb type I insertion. Three of these shorter insertions are flanked on both sides by a short sequence present as a single copy in uninterrupted rDNA units. The duplicated segment is 7, 14 and 15 nucleotides in the different clones. In this respect, the insertions differ from the 5kb type I insertion, where the corresponding sequence is found only at the right hand junction and where at the left hand side there is a deletion of 9 nucleotides of rDNA (Roiha et al.,1981). One clone is unusual in that it contains two type I insertions, one of which is flanked by a 14 nucleotide repeat. The left hand junction of the second insertion occurs 380 nucleotides downstream in the rDNA unit from the first. It has an identical right hand junction to the other elements and the 380 nucleotide rDNA sequence is repeated on both sides of the insertion. We discuss the variety of sequence rearrangements of the rDNA which flank type I insertions.