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: 1.91). 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, Aug 16, 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 · 3.17 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 · 2.48 Impact Factor
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    • "Additionally, telomeric repeat sequences were also present at nontelomeric sites (interstitial telomeric sequences, ITSs). Interstitial telomeric signals were present in 12 pericentromeric regions, coinciding with CBG bands, in P. lamarum and in pair 4 of Phyllomys sp. 4. The origin of ITs is still debated, but it seems that they may reflect components of the satellite DNA, as described in rodents of the genus Microtus (Rovatsos et al. 2011) or remnants of ancestral chromosome rearrangements, such as inversions and centric or tandem fusions (Meyne et al. 1990; Lee et al. 1993; Fagundes et al. 1997; Svartman and Vianna-Morgante 1998; Pellegrino et al. 1999; Bolzán and Bianchi 2006; Ruiz-Herrera et al. 2008). Only three species of Echimyidae (Proechimys gr. "
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    ABSTRACT: Phyllomys (Echimyidae, Rodentia) is a genus of Neotropical rodents with available cytogenetic data restricted to six out of 13 species, mainly based on simple staining methods, without detailed analyses. In this work, we present new karyotypes for Phyllomys lamarum (diploid number 2n = 56, fundamental number or number of autosomal arms FN = 102) and Phyllomys sp. (2n = 74, FN = 140) from the state of Minas Gerais, southeastern Brazil. We provide the first GTG- and CBG-banding patterns, silver-staining of the nucleolar organizer regions (Ag-NORs), and fluorescence in situ hybridization (FISH) with telomeric and 45S rDNA probes of Phyllomys. In addition to examining their chromosomes and phenotypic characters, we sequenced mitochondrial DNA from the specimens analyzed to confirm their taxonomic identification. The comparison of the distinctive chromosome complements of our specimens with those of other species of Phyllomys already published allowed us to conclude that chromosome data may be very useful for the taxonomy of the genus, as no two species analyzed presented the same diploid and fundamental numbers (2n and FN).
    Genome 01/2014; 57(1):1-8. DOI:10.1139/gen-2013-0168 · 1.56 Impact Factor
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