Satellite DNAs represent the most abundant fraction of repetitive sequences in genomes of almost all eukaryotic species. Long arrays of satellite DNA monomers form densely packed heterochromatic genome compartments and also span over the functionally important centromere locus. Many specific features can be ascribed to the evolution of tandemly repeated genomic components. This chapter focuses on the structural and evolutionary dynamics of satellite DNAs and the potential molecular mechanisms responsible for rapid changes of the genomic areas they constitute. Monomer sequences of a satellite DNA evolve concertedly through a process of molecular drive in which mutations are homogenized in a genome and fixed in a population. This process results in divergence of satellite sequences in reproductively isolated groups of organisms. However, some satellite DNA sequences are conserved over long evolutionary periods. Since many satellite DNAs exist in a genome, the evolution of species-specific satellite DNA composition can be directed by copy number changes within a library of satellite sequences common for a group of species. There are 2 important features of these satellite DNAs: long time sequence conservation and, at the same time, proneness to rapid changes through copy number alterations. Sequence conservation may be enhanced by constraints such as those imposed on functional motifs and/or architectural features of a satellite DNA molecule. Such features can limit the selection of sequences able to persist in a genome, and can direct the evolutionary course of satellite DNAs spanning the functional centromeres.

The centromere is a chromosomal locus responsible for the faithful segregation of genetic material during cell division. It has become evident that centromeres can be established literally on any DNA sequence, and the possible synergy between DNA sequences and the most prominent centromere identifiers, protein components, and epigenetic marks remains uncertain. However, some evolutionary preferences seem to exist, and long-term established centromeres are frequently formed on long arrays of satellite DNAs and/or transposable elements. Recent progress in understanding functional centromere sequences is based largely on the high-resolution DNA mapping of sequences that interact with the centromere-specific histone H3 variant, the most reliable marker of active centromeres. In addition, sequence assembly and mapping of large repetitive centromeric regions, as well as comparative genome analyses offer insight into their complex organization and evolution. The rapidly advancing field of transcription in centromere regions highlights the functional importance of centromeric transcripts. Here, we comprehensively review the current state of knowledge on the composition and functionality of DNA sequences underlying active centromeres and discuss their contribution to the functioning of different centromere types in higher eukaryotes.

Human centromeres contain multi-megabase-sized arrays of alpha satellite DNA, a family of satellite DNA repeats based on a tandemly arranged 171bp monomer. The centromere-specific histone protein CENP-A is assembled on alpha satellite DNA within the primary constriction, but does not extend along its entire length. CENP-A domains are estimated to extend over 1500-2000kb of alpha satellite DNA. However, these estimates do not take into account inter-individual variation in alpha satellite array sizes on homologous chromosomes and among different chromosomes. We defined the genomic distance of CENP-A chromatin on human chromosomes X and Y from different individuals. CENP-A chromatin occupied different genomic intervals on different chromosomes, but despite inter-chromosomal and inter-individual array size variation, the ratio of CENP-A to total alpha satellite DNA size remained consistent. Changes in the ratio of alpha satellite array size to CENP-A domain size were observed when CENP-A was over-expressed and when primary cells were transformed by disrupting interactions between the tumor suppressor protein Rb and chromatin. Our data support a model for centromeric domain organization in which the genomic limits of CENP-A chromatin varies on different human chromosomes, and imply that alpha satellite array size is a more prominent predictor of CENP-A incorporation than chromosome size. In addition, our results also suggest that cancer transformation and amounts of centromeric heterochromatin have notable effects on the amount of alpha satellite that is associated with CENP-A chromatin.

Transposable elements (TEs) and satellite DNAs (satDNAs) are typically identified as major repetitive DNA components in eukaryotic genomes. TEs are DNA segments able to move throughout a genome while satDNAs are tandemly repeated sequences organized in long arrays. Both classes of repetitive sequences are extremely diverse, and many TEs and satDNAs exist within a genome. Although they differ in structure, genomic organization, mechanisms of spread, and evolutionary dynamics, TEs and satDNAs can share sequence similarity and organizational patterns, thus indicating that complex mutual relationships can determine their evolution, and ultimately define roles they might have on genome architecture and function. Motivated by accumulating data about sequence elements that incorporate features of both TEs and satDNAs, here we present an overview of their structural and functional liaisons.