Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.

The Importance of Cancer Cell Lines as in vitro Models in Cancer Methylome Analysis and Anticancer Drugs Testing | InTechOpen, Published on: 2013-03-13. Authors: Daniela Ferreira, Filomena Adega and Raquel Chaves

In recent years, a growing body of evidence has recognized the tandem repeat sequences, and specifically satellite DNA, as a functional class of sequences in the genomic “dark matter.” Using an original, complementary, and thus an eclectic experimental design, we show that the cat archetypal satellite DNA sequence, FA-SAT, is “frozen” conservatively in several Bilateria genomes. We found different genomic FA-SAT architectures, and the interspersion pattern was conserved. In Carnivora genomes, the FA-SAT-related sequences are also amplified, with the predominance of a specific FA-SAT variant, at the heterochromatic regions. We inspected the cat genome project to locate FA-SAT array flanking regions and revealed an intensive intermingling with transposable elements. Our results also show that FA-SAT-related sequences are transcribed and that the most abundant FA-SAT variant is not always the most transcribed. We thus conclude that the DNA sequences of FA-SAT and their transcripts are “frozen” in these genomes. Future work is needed to disclose any putative function that these sequences may play in these genomes.

Despite the many questions regarding satellite DNA sequences and their cellular roles, the evolutionary history of eukaryotic genomes seems to have been largely influenced by this dynamic and multifaceted genomic component. The bovine genome is highly rich in diverse satDNA sequences that differ in monomer sequence and length, complexity, chromosomal location and abundance, as well as in their sequences’ evolutionary mechanisms. In the evolution of the Bovidae family, the genomes’ repetitive fraction played a central role in karyotype reorganisation, and in the last few decades several studies have demonstrated and reinforced an association between centromeric satDNAs and the process of chromosome evolution in remodelling genomes of Bovidae species. Here, we review different aspects of the molecular nature and genome behaviour of all the satDNA families identified in the bovine genome, including their organisation, abundance, chromosome localisation, variation in sequence, and evolutionary history in the Bovidae family and in particular in the Bovinae subfamily, taking an integrative perspective. “Evolution and satDNA” can be addressed through two complementary views: the satDNA sequence evolution per se, and genome evolution promoted by the satDNA dynamism. SatDNA both provides phylogenetic information and is a critical genomic component that enables sequence and chromosome evolution – features arising from its presence, absence or alteration.