Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA

Abstract

Satellite DNA sequences are known to be important components required for the construction of centromeres and are common to all higher eukaryotes. Nevertheless, their nucleotide sequences vary significantly, even in evolutionarily related species. In order to elucidate how the nucleotide sequences define the conformational character of centromeric satellite DNA, an evolutionary path toward repetitive units has been hypothesized. In that context, the DNA conformation of fish satellite DNA was evaluated in two ways: the organization of subrepeats and sequence characteristics were compared, and the differences in stacking energies between A-helix and B-helix and the sequence-dependent bendability of the helices were evaluated. Our findings suggest that the monomeric units making up currently observed repetitive sequences have evolved through stepwise amplification of shorter, ancestral sequences by increasing the length of the units. In addition, we suggest that potentially key sequences required for DNA amplification comprise highly flexible structures. Thus flexibility of the DNA structure may be a primary prerequisite for DNA amplification.

A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes: Erythrinidae) is derived from 5S rDNA

“…An extensive analysis of centromeric satellite DNAs of vertebrates showed the presence of short A-rich motifs, typical characteristics of centromere satellite (Vina˜s et al, 2004). The expanded TAAA motif in the 5SHindIII-DNA is similar to the short A-rich motifs that were previously identified in the centromeric satellite DNAs of different fish species (Wright, 1989;Denovan and Wright, 1990;Garrido-Ramos et al, 1995;Kato, 1999;Canapa et al, 2002;Vin˜as et al, 2004). These short sequences are quite similar showing considerable similarity to other centromeric motifs found in human (Vissel, Nagy and Choo, 1992), mouse (Wong and Rattner, 1988), and reptiles (Cremisi et al, 1988), suggesting that such sequences might play any important role in the structure and function of the H. malabaricus centromere.…”

Comparative chromosome mapping of 5S rDNA and 5S<i>Hin</i>dIII repetitive sequences in Erythrinidae fishes (Characiformes) with emphasis on the <i>Hoplias malabaricus</i> ‘species complex’

“…An extensive analysis of centromeric satellite DNAs of vertebrates showed the presence of typical short A-rich motifs (Viñas et al, 2004). The expanded TAAA motif in the 5S Hin dIII-DNA is similar to the short A-rich motifs that were previously identified in the centromeric satellite DNAs of different fish species (Wright, 1989;Denovan and Wright, 1990;Garrido-Ramos et al, 1995;Kato, 1999;Canapa et al, 2002;Viñas et al, 2004). This short motif also shows considerable similarity to other centromeric motifs found in humans (Vissel et al, 1992), mice (Wong and Rattner, 1988), and reptiles (Cremisi et al, 1988), suggesting that such sequences might play an important role in the structure and function of the H. malabaricus centromere.…”

Slow evolving satellite DNAs: the case of a centromeric satellite in Chalcides ocellatus (Forskål, 1775) (Reptilia, Scincidae)

“…This kind of dinucleotides and adenin stretches seem to represent recognition sites for High Mobility Group proteins (Garrido-Ramos et al, 1995;Kato, 1999), that may be involved in the organisation of centromeric heterochromatin (Strauss and Varshavsky, 1984;Solomon, Strauss and Varashavsky, 1986;Radie et al, 1992). In addition, GAAA and analogous motifs occur in Hinñ satDNA.…”