Chromosome ends in Chironomus pallidivittatus contain different subfamilies of telomere-associated repeats

Cloning and preliminary verification of telomere-associated sequences in upland cotton

Telomeres are structures enriched in repetitive sequences at the end of chromosomes. In this study, using the telomere primer AA(CCCTAAA)₃CCC for the single primer PCR, two DNA sequences were obtained from Gossypium hirsutum (Linnaeus, 1753) accession (acc.) TM-1. Sequence analysis showed that the two obtained sequences were all rich in A/T base, which was consistent with the characteristic of the telomere-associated sequence (TAS). They were designated as GhTAS1 and GhTAS2 respectively. GhTAS1 is 489 bp long, with 57.6% of A/T, and GhTAS2 is 539 bp long, with 63.9% of A/T. Fluorescence in situ hybridization results showed that both of the cloned TASs were located at the ends of the partial chromosomes of G. hirsutum, with the strong signals, which further confirmed that GhTAS1 and GhTAS2 were telomere-associated sequences including highly tandemly repetitive sequences. Results of blast against the assembled genome of G. hirsutum showed that GhTAS sequences may be missed on some assembled chromosomes. The results provide important evidence for the evaluation of the integrity of assembled chromosome end sequences, and will also contribute to the further perfection of the draft genomes of cotton.

Isolation and characterization of five rice telomere-associated sequences

Acoording to the telomere-repeated sequences of rice, two primers: (TTTAGGG11)(3) and (CCC-TAA.A)(3)CCC were used to amplify rice telomere-assciated sequences (TASs). Fox PCR template preparation. total DNA was digested with restrictive endonuclease and then ligated. Using the ligates or total DNA sa template, eight fragments were obtained with the single primer by the PCR reaction. To confirm that the sequences are derived from telomeric DNA, we conducted Bal31 digestion analysis. Of the eight fragments, seven were susceptible to Bal31 treatment, suggesting that they were TASs. These DNA fragments were further demonstrated u, be rice sub-telomeric sequences by RFLP mapping Five sequences have been mapped to the distal ends on rice chromme 5,6,7 and 9, and two other sequences have been mapped at interstitial sites, suggesting that (TTTAGGG)(n). also exist in the middle of rice chromosomes-All eight fragments were sequenced and characterized.

Canonical TTAGG-repeat telomeres and telomerase in the honey bee, Apis mellifera

The draft assembly of the honey bee Apis mellifera genome sequence reveals that the 17 centromeric-distal telomeres are of a simple, shared, and canonical structure, with 3-4 kb of a unique subtelomeric sequence, followed by several kilobases of TTAGG or variant telomeric repeats. This simple subtelomeric structure differs from the centromeric-proximal telomeres on the short arms of the 15 acrocentric chromosomes, which are apparently composed primarily of the 176-bp AluI tandem repeat. This dichotomy between the distal and proximal telomeres may involve differential participation of the telomeres of the 15 acrocentric chromosomes in the Rabl configuration after mitosis and the chromosome bouquet in meiotic prophase I. As expected from the presence of canonical TTAGG telomeric repeats, we identified a candidate telomerase gene in the bee, as well as the silkmoth Bombyx mori and the flour beetle Tribolium castaneum.

Euchromatic and heterochromatic domains at Drosophila telomeres

Noncoding repetitive sequences make up a large portion of eukaryotic genomes, but their function is not well understood. Large blocks of repetitive DNA-forming heterochromatin around the centromeres are required for this region to function properly, but are difficult to analyze. The smaller regions of heterochromatin at the telomeres provide an opportunity to study their DNA and protein composition. Drosophila telomere length is maintained through the targeted transposition of specific non-long terminal repeat retrotransposons to chromosome ends, where they form long tandem arrays. A subterminal telomere-associated sequence (TAS) lies immediately proximal to the terminal-retrotransposon array. Here, we review the experimental support for the heterochromatic features of Drosophila telomeres, and provide evidence that telomeric regions contain 2 distinct chromatin subdomains: TAS, which exhibits features that resemble beta heterochromatin; and the terminal array of retrotransposons, which appears euchromatic. This organization is significantly different from the telomeric organization of other eukaryotes, where the terminal telomerase-generated repeats are often folded in a t-loop structure and become part of the heterochromatin protein complex.

Uniform distribution of satellite DNA variants on the chromosomes of tenebrionid species Alphitobius diaperinus and Tenebrio molitor

The chromosomes of tenebrionid species Alphitobius diaperinus contain large blocks of pericentromerically located constitutive heterochromatin, as revealed by C-banding procedure. As previously reported, satellite DNA of this species is composed of two related monomeric units organized in three satellite subfamilies. In order to analyze the chromosomal location of the satellite DNA and the distribution of monomeric variants within it, and compare it with the distribution of monomer variants in Tenebrio molitor satellite DNA, the methods of in situ hybridization and restriction enzyme/nick translation were performed. Fluorescent in situ hybridization with the entire satellite DNA reveals the pericentromerically located signals on all chromosomes of the complement, coinciding with heterochromatic blocks. Results of fluorescent in situ hybridization with particular monomeric variants and of in situ restriction enzyme/nick translation show that monomeric variants are homogeneously dispersed within the entire satellite DNA. The spreading of satellite monomeric variants of the related species T. molitor within the pericentromeric heterochromatin of the entire complement, is demonstrated using the method of in situ restriction enzyme/nick translation. Although the complexity of organization of satellite DNAs is quite distinct in these two species, obtained results suggest similar efficiency of mechanisms of spreading and homogenization resulting in random chromosomal distribution of their satellite variants.

Extrachromosomal RNA-DNA complex containing long telomeric repeats in chironomids

We have analysed an extracted RNase sensitive fraction containing telomeric repeat sequences in the telomerase negative dipteran Chironomus tentans. It shows a slow and well-defined electophoretic migration corresponding to > 20 kb and is sensitive not only to RNase, but also to DNase. It hybridizes to both strands of the telomeric repeat with about equal intensities. DNA is probably the dominant component since the fraction is only slightly heavier than genomic DNA in isopycnic gradients but considerably lighter than RNA. It can, nevertheless, be shown to incorporate tritiated uridine. The material might represent another example of extrachromosomal telomeric repeats in telomerase negative cells.

DNA structures common for chironomid telomeres terminating with complex repeats

Tandem repeats, 340 bp long, have been shown to terminate the chromosomes in Chironomus pallidivittatus and similar DNA may be used for this purpose by related insects. In view of the importance of Chironomus in telomere studies, representing in principle a third system after short repeats and Drosophila telomeric retrotransposons, we have investigated the related Chironomus dilutus, to learn what DNA structures are conserved at the chromosome ends. Interspersed subrepeats in the telomeric repeats, which contain a long palindrome, and a zone of about 100 bp of relatively constant subtelomeric DNA towards the junction to the telomeric DNA, are characteristic for C. dilutus as for previously investigated species. C. dilutus has similar subtelomeric DNA at all chromosome ends, but typical telomeric repeats in only seven of the pairs since the eighth telocentric pair contains centromere-specific repeats.

Interspersed DNA element restricted to a specific group of telomeres in the dipteran Chironomus pallidivittatus

Telomeres in the dipteran Chironomus pallidivittatus terminate with 340bp tandem DNA repeats belonging to different subfamilies with characteristic intertelomeric distribution. We have now found, interspersed between such repeats, a composite element of approx. 1400bp present in two similar size variants, with several components of nontelomeric origin. There were about 50 copies of the element, predominantly or exclusively present in a previously defined group of telomeres, characterized by a unique set of telomeric tandem repeat subfamilies. Elements were integrated at irregular distances from each other, and intervening telomeric tandem repeat DNA was variable in composition. Nevertheless, the flanks immediately surrounding the elements were identical for different elements; in other words, there was a site-specific insertion. We suggest that this selective invasion of a small part of the genome by an interspersed, probably rapidly evolving element is best explained by repeated gene conversions.

Telomeres terminating with long complex tandem repeats

Telomeres of most investigated species terminate with short repeats and are elongated by telomerase. Short repeats have never been detected in dipteran species which have found other solutions to end a chromosome. Whereas in Drosophila melanogaster retroelements are added onto the termini, chironomids have long complex repeats at their chromosome ends. We review evidence that these units are terminal and probably have evolved from short telomeric repeats. In Chironomus pallidivittatus the units have been shown to belong to different subfamilies which have specific inter- and intrachromosomal distribution, the most terminal subfamily of repeats being characterized by pronounced secondary structures for the single strand. The complex repeats are efficiently homogenized both within and between different chromosome ends. Gene conversion is probably an important component in the coordinate evolution of the repeats but it is not known whether it is used for net synthesis of DNA. RNA is used as an intermediate in telomere elongation both by organisms having chromosomes terminating with short repeats and by D. melanogaster. It is therefore interesting that the terminal repeats in chironomids are transcribed.

Terminal long tandem repeats in chromosomes form Chironomus pallidivittatus

We provide evidence that a chromosome end in the dipteran Chironomus pallidivittatus contains 340-bp tandem repeats reaching the extreme terminus of the chromosome. After adding synthetic oligonucleotide tails to DNA extracted from the microdissected right end of the fourth chromosome, we could demonstrate that the blocks of repeats were tailed at only one end, the chromosome terminus, the interior of the arrays being unavailable for tailing. Using PCR, we furthermore showed that the added tails were connected to 340-bp repeat DNA directly, i.e., without intervening DNA of any other kind. The tailed repeats belong to a subfamily previously known to be the most peripheral one of the different types of 340-bp units. Using plasmid controls, we could also make certain that we did not amplify rare or nonrepresentative DNA termini.

Molecular characterization of the Anopheles gambiae 2L telomeric region via an integrated transgene

A Drosophila P-element derivative (pUChsneo) integrated into the telomeric region of the left arm of the second chromosome of Anopheles gambiae was used to clone the proximally flanking An. gambiae sequences. Molecular analyses revealed that the pUChsneo construct was partially duplicated and had integrated into a subterminal minisatellite. This satellite has a repeat unit of 820 bp and is located exclusively at the tip of 2L. No sequence similarity to subterminal minisatellites from other dipterans was detected, but some structural features such as tandem subrepeats are shared. The end of the chromosome was mapped with respect to restriction sites in pUChsneo at approximately generation 100 after the integration event. Considering inevitable terminal nucleotide loss due to incomplete DNA replication, we conclude that the chromosome end must have undergone a dramatic elongation process since it was mapped in generation 23.

DNA organization and polymorphism of a wild-type Drosophila telomere region

Telomeres at the ends of linear chromosomes of eukaryotes protect the chromosome termini from degradation and fusion. While telomeric replication/elongation mechanisms have been studied extensively, the functions of subterminal sequences are less well understood. In general, subterminal regions can be quite polymorphic, varying in size from organism to organism, and differing among chromosomes within an organism. The subterminal regions of Drosophila melanogaster are not well characterized today, and it is not known which and how many different components they contain. Here we present the molecular characterization of DNA components and their organization in the subterminal region of the left arm of chromosome 2 of the Oregon RC wild-type strain of D. melanogaster, including a minisatellite with a 457bp repeat length. Two distinct polymorphic arrangements at 2L were found and analyzed, supporting the Drosophila telomere elongation model by retrotransposition. The high incidence of terminal chromosome deficiencies occurring in natural Drosophila populations is discussed in view of the telomere structure at 2L.

A family of complex tandem DNA repeats in the telomeres of Chironomus pallidivittatus

A family of 340-bp tandem telomere-associated DNA repeats is present in 50- to 200-kb blocks in seven of the eight paired chromosome ends in Chironomus pallidivittatus. It consists of four main subfamilies, differing from each other by small clusters of mutations. This differentiation may reflect different functional roles for the repeats. Here we find that one subfamily, D3, is consistently localized most peripherally and extends close to the ends of the chromosomes, as shown by its sensitivity to the exonuclease Bal 31. The amounts of D3 are highly variable between individuals. The repeat characteristic for D3 forms a segment with pronounced dyad symmetry, which in single-strand form would give rise to a hairpin. Evidence from an interspecies comparison suggests that a similar structure is the result of selective forces. Another subfamily, M1, is present more proximally in a subgroup of telomeres characterized by a special kind of repeat variability. Thus, a complex block with three kinds of subfamilies may occupy different M1 telomeres depending on the stock of animals. We conclude that subfamilies are differentially distributed between and within telomeres and are likely to serve different functions.

A family of complex tandem DNA repeats in the telomeres of Chironomus pallidivittatus

A family of 340-bp tandem telomere-associated DNA repeats is present in 50- to 200-kb blocks in seven of the eight paired chromosome ends in Chironomus pallidivittatus. It consists of four main subfamilies, differing from each other by small clusters of mutations. This differentiation may reflect different functional roles for the repeats. Here we find that one subfamily, D3, is consistently localized most peripherally and extends close to the ends of the chromosomes, as shown by its sensitivity to the exonuclease Bal 31. The amounts of D3 are highly variable between individuals. The repeat characteristic for D3 forms a segment with pronounced dyad symmetry, which in single-strand form would give rise to a hairpin. Evidence from an interspecies comparison suggests that a similar structure is the result of selective forces. Another subfamily, M1, is present more proximally in a subgroup of telomeres characterized by a special kind of repeat variability. Thus, a complex block with three kinds of subfamilies may occupy different M1 telomeres depending on the stock of animals. We conclude that subfamilies are differentially distributed between and within telomeres and are likely to serve different functions.

The genomic organization of HeT-A retroposons in Drosophila melanogaster

Members of the Drosophila HeT-A family of transposable elements are LINE-like retroposons that are found at telomeres and in centric heterochromatin. We recently characterized an active HeT-A element that had transposed to a broken chromosome end fewer than nine generations before it was isolated. The sequence arrangement of this element, called 9D4, most likely represents the organization of an actively transposing member of the HeT-A family. Here we assess the degree of divergence among members of the HeT-A family and test a model of telomere length maintenance based on HeT-A transposition. The region containing the single open reading frame of this element appears to be more highly conserved than the non-coding regions. The HeT-A element has been implicated in the Drosophila telomere elongation process, because frequent transpositions to chromosome ends are sufficient to counter-balance nucleotide loss due to incomplete DNA replication. The proposed elongation model and the hypothetical mechanism of HeT-A transposition predict a predominant orientation of HeT-A elements with their oligo (A) tails facing proximally at chromosome ends, as well as the existence of irregular tandem arrays of HeT-A elements at chromosome ends resulting from transposition of new HeT-A elements onto chromosome ends with existing elements. Twenty-nine different HeT-A fragments were isolated from directional libraries that were enriched in terminal DNA fragments. Sequence analyses of these fragments and comparisons with the organization of the HeT-A element, 9D4, fit these two predictions and support the model of Drosophila telomere elongation by transposition of HeT-A elements.

A repetitive DNA sequence associated with the centromeres of Chironomus pallidivittatus

A clone containing centromere-associated DNA from Chironomus pallidivittatus was obtained by microdissection-microcloning. It hybridizes to the centromeric end of one chromosome and exclusively to regions in the three remaining, metacentric chromosomes to which centromeres have previously been localized on cytological grounds. In the metacentric positions the hybridization can be assigned to thin bands. The clone contains 155bp tandem repeats and short flanking regions represented in all of the centromeres. Titration experiments show that the four centromeres together contain 200kb of 155bp repeat per genome. In a line of tissue culture cells the amounts are increased by a factor 1.5-2, resulting in proportionately extended arrays of tandem repeats. Each repeat contains two invertrepeats surrounding a region containing only AT base pairs, a feature with some similarity to functionally essential elements in the Saccharomyces cerevisiae centromere.

Complex telomere-associated repeat units in members of the genus Chironomus evolve from sequences similar to simple telomeric repeats

The dipteran Chironomus tentans has complex tandemly repeated 350-bp DNA sequences at or near the chromosome ends. As in Drosophila melanogaster, short simple repeats with cytosines and guanines in different strands have never been observed. We were therefore interested in learning whether the Chironomus repeats could have evolved from simple sequence telomeric DNA, which might suggest that they constitute a functional equivalent. We screened for repeat units with evolutionarily ancient features within the tandem arrays and recovered two clones with a less-evolved structure. Sequence analysis reveals that the present-day 350-bp unit probably evolved from a simpler 165-bp unit through the acquisition of transposed sequences. The 165-bp unit contains DNA with a highly biased distribution of cytosine and guanine between the two strands, although with the ratios inverted in two minor parts of the repeat. It is largely built up of short degenerate subrepeats for which most of the sequence can be reconstructed. The consensus for the subrepeat sequence is similar to the simple telomeric repeat sequences of several kinds of eukaryotes. We propose that the present-day unit has evolved from telomeric, simple sequence, asymmetric DNA from which it has retained some original sequence features and possibly functions.

Complex telomere-associated repeat units in members of the genus Chironomus evolve from sequences similar to simple telomeric repeats

The dipteran Chironomus tentans has complex tandemly repeated 350-bp DNA sequences at or near the chromosome ends. As in Drosophila melanogaster, short simple repeats with cytosines and guanines in different strands have never been observed. We were therefore interested in learning whether the Chironomus repeats could have evolved from simple sequence telomeric DNA, which might suggest that they constitute a functional equivalent. We screened for repeat units with evolutionarily ancient features within the tandem arrays and recovered two clones with a less-evolved structure. Sequence analysis reveals that the present-day 350-bp unit probably evolved from a simpler 165-bp unit through the acquisition of transposed sequences. The 165-bp unit contains DNA with a highly biased distribution of cytosine and guanine between the two strands, although with the ratios inverted in two minor parts of the repeat. It is largely built up of short degenerate subrepeats for which most of the sequence can be reconstructed. The consensus for the subrepeat sequence is similar to the simple telomeric repeat sequences of several kinds of eukaryotes. We propose that the present-day unit has evolved from telomeric, simple sequence, asymmetric DNA from which it has retained some original sequence features and possibly functions.