Tandemly repeated DNA sequences and the centromeres

Arrays of DNA sequences repeated in tandem, commonly known as satellite DNAs (satDNAs), build heterochromatic chromosomal compartments of almost every eukaryotic species. Many satDNAs differing in sequence, copy number, and chromosomal localization populate a genome. Non- coding character, repetitiveness, difficulties in cloning, sequencing and assembly of hundreds and thousands of nearly-identical monomers made these sequences poorly explored, particularly regarding their possible roles in genome function and evolution. Tandem repeats are a preferred form of DNA sequences in pericentromeres, spanning also the functional centromere, a domain responsible for proper segregation of chromosomes in cell divisions. However, there is no particular centromeric DNA, and centromeres are epigenetically determined by histone H3 protein variant CENH3. CENH3 is also a species-specific marker of centromere function, owing to the association of its rapidly evolving N-terminal part with underlying DNA sequences. According to the library model, species-specific differences in satDNA composition are explained as a result of copy number alterations within a set, regularly shared by a group of related species. In addition, evolution of satDNA nucleotide sequences can be surprisingly slow, and some can persist for extremely long evolutionary periods. Features of satDNA sequence dynamics might be advantageous for maintaining DNA-protein interactions in the centromere, allowing in the same time rapid replacements and stability of satDNA variants. To keep functionality, both DNA and protein components must evolve in accord, and they drive each other’s evolution. Once accumulated in groups of individuals, changes in the centromeric satDNA and in the corresponding CENH3 can cause incompatibilities in chromosome pairing in hybrids, thus triggering reproductive isolation and speciation. Recent advances in NGS sequencing and in bioinformatic tools enabled characterization of a whole-genome complement of satellite DNAs, the satellitome. In combination with chromatin immunoprecipitation using CENH3- specific antibodies, it is now possible to focus onto details of composition of DNA sequences within and around centromeres of a variety of experimental organisms.