Sequence, Chromatin and Evolution of Satellite DNA

Abstract

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5-10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

Keywords: CENP-A; H3K9me3; centromeres; heterochromatin; non-B-form DNA; repetitive DNA; telomeres.

Figure 1

Sequence motifs, basic organizational units and predicted non-B-form secondary DNA structures on various functional classes of satellite DNA.

Figure 2

Satellite chromatin organization. In contrast to euchromatin, pericentric and subtelomeric regions are compact, marked by repressive modifications such as H3K9me3 and H3K20me3 and bound by Heterochromatin-associated Protein 1 (HP1). At centromeres, Centromere Protein A (CENP-A) nucleosomes form tight complexes with DNA binding centromeric proteins CENP-B, CENP-C and the histone-fold containing protein complex CENP-TWSX. Telomeric ends contain irregularly spaced and tightly packed nucleosomes separated by 10-20 bp DNA linkers. Telomeric chromatin is tightly associated with the shelterin complex and HP1.

Figure 3

Satellite evolution. The library model can account for the divergent evolution of species-specific satellite families through independent expansion and contraction of satellite families in diverging species. Concerted evolution occurs via recombinational processes that result in expansions, contractions and homogenizations of tandemly repetitive sequences. Centromere drive is a selfish process in which stronger centromeres preferentially orient towards the egg pole during asymmetric female meiosis. Drive is suppressed when mutation of a centromere-binding protein restores centromere balance, resulting in an arms race between centromeric satellite DNA and centromere proteins.