Telomeric repeats far from the ends: mechanisms of origin and role in evolution. Cytogenet Genome Res

Dipartimento di Genetica e Microbiologia, Adriano Buzzati-Traverso, Università di Pavia, Pavia, Italy.
Cytogenetic and Genome Research (Impact Factor: 1.56). 02/2008; 122(3-4):219-28. DOI: 10.1159/000167807
Source: PubMed

ABSTRACT In addition to their location at terminal positions, telomeric-like repeats are also present at internal sites of the chromosomes (intrachromosomal or interstitial telomeric sequences, ITSs). According to their sequence organization and genomic location, two different kinds of ITSs can be identified: (1) heterochromatic ITSs (het-ITSs), large (up to hundreds of kb) stretches of telomeric-like DNA localized mainly at centromeres, and (2) short ITSs (s-ITSs), short stretches of telomeric hexamers distributed at internal sites of the chromosomes. Het-ITSs have been only described in some vertebrate species and they probably represent the remnants of evolutionary chromosomal rearrangements. On the contrary, s-ITSs are probably present in all mammalian genomes although they have been described in detail only in some completely sequenced genomes. Sequence database analysis revealed the presence of 83, 79, 244 and 250 such s-ITSs in the human, chimpanzee, mouse and rat genomes, respectively. Analysis of the flanking sequences suggested that s-ITSs were inserted during the repair of DNA double-strand breaks that occurred in the course of evolution. An extensive comparative analysis of the s-ITS loci and their orthologous 'empty' loci confirmed this hypothesis and suggested that the repair event involved the direct action of telomerase. Whereas het-ITSs seem to be intrinsically prone to breakage, the instability of s-ITSs is more controversial. This observation is consistent with the hypothesis that s-ITSs are probably not themselves prone to breakage but represent 'scars' of ancient breakage that may have occurred within fragile regions. This study will review the current knowledge on these two types of ITS, their molecular organization, how they arose during evolution, their implications for chromosomal instability and their potential applications as phylogenetic/forensic markers.

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Available from: Aurora Ruiz-Herrera, Sep 29, 2015
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    • "It has been suggested that from many ITRs, only large blocks of telomeric repeats (spanning several hundred kb) are involved in chromosome breakage, whereas instability of short ITRs is more controversial (Lin and Yan 2008; Ruiz-Herrera et al. 2008). ITRs observed in P. echinatum definitely contain a high number of repeats because FISH performed on condensed chromosomes cannot detect target loci smaller than 10 kb. "
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    ABSTRACT: Phleum echinatum Host (2n = 2x = 10) is an annual Mediterranean species which differs from other representatives of the genus Phleum by reduced chromosome number, asymmetric karyotype and unusually high amount of DNA in the genome. Chromosomes of this plant were studied using conventional acetic-orcein staining and fluorescence in situ hybridization (FISH). FISH showed the major 35S ribosomal DNA (rDNA) site at the secondary constriction of satellite chromosome (3) and the minor 35S rDNA site near 5S rDNA cluster in the monobrachial chromosome 5. Telomeric repeats were detected at all chromosome ends within secondary constriction in satellited chromosome 3 and at the centromeric regions of chromosomes 1 and 2. Intrachromosomally located telomeric repeats are probably traces of chromosomal rearrangements that have shaped P.echinatum genome; they were prone to breakage which was manifested in chromosome fragmentation. The most distinct telomeric signals, suggesting massive amplification of interstitial telomeric sequences (ITRs), were observed at the nucleolar organizer region (NOR) of the third chromosome pair. Double FISH confirmed co-localization of telomeric and 35S rDNA repeats in this locus characterized by the biggest fragility in the karyotype. Fragile sites of P.echinatum, composed of amplified telomeric repeats, may bear a resemblance to metazoan rare fragile sites enriched in microsatellite repeats. Electronic supplementary material The online version of this article (doi:10.1007/s00709-014-0681-5) contains supplementary material, which is available to authorized users.
    Protoplasma 07/2014; 252(1). DOI:10.1007/s00709-014-0681-5 · 2.65 Impact Factor
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    • "Chromosomal mapping of telomeric sequences has been widely used to identify chromosomal rearrangements among karyotypes of vertebrates and to detect fusion and/or fission, inversion or translocation events [10-16]. Many recent studies have emphasized the important role of this sequence in chromosomal evolution [17-19], and many studies have reported that sequences related to telomeric sequences form a component of satellite DNA [20-22]. "
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    ABSTRACT: The combination of classical cytogenetics with molecular techniques represents a powerful approach for the comparative analysis of the genome, providing data for the systematic identification of chromosomal homologies among species and insights into patterns of chromosomal evolution within phylogenetically related groups. Here, we present cytogenetic data on four species of Neotropical treefrogs of the genus Phyllomedusa (P. vaillantii, P. tarsius, P. distincta, and P. bahiana), collected in Brazil and Ecuador, with the aim of contributing to the understanding of the chromosomal diversification of this genus. With the exception of P. tarsius, which presented three telocentric pairs, all the species analyzed had conservative karyotypic features. Heterochromatic patterns in the genomes of these species revealed by C-banding and fluorochrome staining indicated the presence of a large number of non-centromeric blocks. Using the Ag-NOR method and FISH with an rDNA 28S probe, we detected NOR in the pericentromeric region of the short arm of pair 7 in P. vaillantii, pair 1 in P. tarsius, chromosomes 1 and 9 in P. distincta, and in chromosome 9 in P. bahiana, in addition to the presence of NOR in one homologue of chromosome pair 10 in some individuals of this species. As expected, the telomeric probe detected the terminal regions of the chromosomes of these four species, although it also detected Interstitial Telomeric Sequences (ITS) in some chromosomes of the P. vaillantii, P. distincta and P. bahiana karyotypes. A number of conservative chromosomal structures permitted the recognition of karyotypic homologies. The data indicate that the presence of a NOR-bearing chromosome in pair 9 is the plesiomorphic condition in the P. burmeisteri group. The interspecific and intraspecific variation in the number and location of rDNA sites reflects the rapid rate of evolution of this character in Phyllomedusa. The ITS detected in this study does not appear to be a remnant of structural chromosome rearrangements. Telomeric repeats were frequently found in association with heterochromatin regions, primarily in the centromeres, which suggests that (TTAGGG)n repeats might be an important component of this heterochromatin. We propose that the ITSs originated independently during the chromosomal evolution of these species and may provide important insights into the role of these repeats in vertebrate karyotype diversification.
    Molecular Cytogenetics 03/2014; 7(1):22. DOI:10.1186/1755-8166-7-22 · 2.14 Impact Factor
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    • "The occurrence of chromosomal fusion is also reinforced by the presence of ITS at centromeric regions of pair 2 interpreted as remains of telomere sequences in rearranged chromosomes that have been amplified and maintained during speciation of Trinectes inscriptus. This unusual chromosomal organization represents hotspots for karyotype changes once they are supposed to act as alternative sites for telomere formation (Meyne et al., 1990; Ruiz-Herrera et al., 2008). Once telomere sequences are usually degenerated or modified into heterochromatin after internalization (Colomba et al., 2002; Cross et al., 2006; Ocalewicz, 2013), we infer that the fusion responsible for the origin of pair 2 in T. inscriptus is more recent than those proposed for pairs 1 and 3. "
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    ABSTRACT: Flatfish (Pleuronectiformes) are one of the few examples of marine fish with remarkable chromosomal variation. Nonetheless, cytogenetic data in species of this order are still scarce and population approaches have been neglected. Therefore, a detailed karyotypic survey was carried out for the first time in Trinectes inscriptus along northeastern and southeastern Brazil. All specimens shared 2n = 42 with a karyotype composed of eight metacentric/submetacentric and 34 subtelocentric/acrocentric chromosomes, differing from the basal condition of marine teleosteans (48 acrocentric chromosomes). Heterochromatin was restricted to the pericentromeric region of most chromosomes, short arms of a few pairs and coincident with GC-rich sites at NORs. Fluorescence in situ hybridization (FISH) using 18S and 5S rDNA probes revealed synteny between both rDNA classes at pair 5 in all samples. Telomeric sequences were mapped at terminal sites of most chromosomes as well as at centromeric region of the second pair. The derived karyotype macrostructure reported in T. inscriptus (low 2n, presence of large biarmed chromosomes) has probably evolved from chromosomal fusions, as reinforced by the presence of internal telomere sequences (ITS) in a large metacentric pair, besides inversions and heterochromatin accumulation. Since this pattern of genomic organization was stable among collection sites (up to 1000 km apart), we suggest these rearrangements have taken place in the beginning of species diversification.
    Journal of Experimental Marine Biology and Ecology 03/2014; 452:101–104. DOI:10.1016/j.jembe.2013.12.012 · 1.87 Impact Factor
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