Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective

Abstract

Interstitial telomeric sequences (ITSs) are short stretches of telomeric-like repeats (TTAGGG)n at nonterminal chromosomal sites. We previously demonstrated that, in the genomes of primates and rodents, ITSs were inserted during the repair of DNA double-strand breaks. These conclusions were derived from sequence comparisons of ITS-containing loci and ITS-less orthologous loci in different species. To our knowledge, insertion polymorphism of ITSs, i.e., the presence of an ITS-containing allele and an ITS-less allele in the same species, has not been described. In this work, we carried out a genome-wide analysis of 2504 human genomic sequences retrieved from the 1000 Genomes Project and a PCR-based analysis of 209 human DNA samples. In spite of the large number of individual genomes analyzed we did not find any evidence of insertion polymorphism in the human population. On the contrary, the analysis of ITS loci in the genome of a single horse individual, the reference genome, allowed us to identify five heterozygous ITS loci, suggesting that insertion polymorphism of ITSs is an important source of genetic variability in this species. Finally, following a comparative sequence analysis of horse ITSs and of their orthologous empty loci in other Perissodactyla, we propose models for the mechanism of ITS insertion during the evolution of this order.

Telomeric-Like Repeats Flanked by Sequences Retrotranscribed from the Telomerase RNA Inserted at DNA Double-Strand Break Sites during Vertebrate Genome Evolution

“…Following these findings, we proposed that s-ITSs were inserted in genomes through a peculiar pathway of DNA double-strand break repair [32]. Our work on ITS loci in rodents [34] and equids [35] provided further evidence for this hypothesis. We then tested whether s-ITSs can be inserted at DNA doublestrand breaks in cultured somatic cells by inducing site-specific breaks catalyzed by the enzyme I-SceI [36].…”

“…Given the limited number of repeats at these loci, their detection by FISH, using telomeric probes, is inefficient and they have mainly been identified through genome sequence analysis. We previously studied s-ITSs in primates [29][30][31][32][33][34], rodents [34], and perissodactyls [35]. S-ITS can be considered a particular type of microsatellite composed of the repetition of 6 bp long units.…”

“…At these loci, the telomeric repeat stretch is flanked by a sequence reverse transcribed from the 3 domain of TERC [34]. We recently identified a TERC-ITS locus in the horse genome which contains a sequence derived from the pseudoknot [35]. The peculiar organization of these loci strongly suggested that the telomerase enzyme may be involved in their insertion of ITSs in genomes.…”

Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings

“…Difficulty of interpretation is probably one of the reasons why fragile sites or chromosome breaks have not been included in any equine clinical cytogenetic case report, even though breaks and gaps have been observed and recorded in laboratory notes (TAMUMCL archive). Fragile sites certainly deserve further attention by clinical cytogenetics and basic genome research because in both humans and horses, they have been co-localized with interstitial telomeric sequences, known as genomic ‘scars’ marking DNA break/repair sites and possibly more unstable genomic regions [ 121 ].…”

Interstitial Telomeric Repeats Are Rare in Turtles

“…Some authors classified ITRs into two main groups: the short ITRs (s-ITRs) and the heterochromatic ITRs (Het-ITRs) [15]. Other authors report a more detailed classification including s-ITRs, subtelomeric ITRs, fusion ITRs and pericentromeric ITRs [14][15][16][17][18]. s-ITRs are characterized by a low copy number of (TTAGGG) n tandem repeats, located in interstitial positions of the chromosomes.…”