Functional Significance of Satellite DNAs: Insights From Drosophila

Abstract

Since their discovery more than 60 years ago, satellite repeats are still one of the most enigmatic parts of eukaryotic genomes. Being non-coding DNA, satellites were earlier considered to be non-functional "junk," but recently this concept has been extensively revised. Satellite DNA contributes to the essential processes of formation of crucial chromosome structures, heterochromatin establishment, dosage compensation, reproductive isolation, genome stability and development. Genomic abundance of satellites is under stabilizing selection owing of their role in the maintenance of vital regions of the genome-centromeres, pericentromeric regions, and telomeres. Many satellites are transcribed with the generation of long or small non-coding RNAs. Misregulation of their expression is found to lead to various defects in the maintenance of genomic architecture, chromosome segregation and gametogenesis. This review summarizes our current knowledge concerning satellite functions, the mechanisms of regulation and evolution of satellites, focusing on recent findings in Drosophila. We discuss here experimental and bioinformatics data obtained in Drosophila in recent years, suggesting relevance of our analysis to a wide range of eukaryotic organisms.

Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy

“…Numerous genome studies have shown the ubiquity and abundance of repetitive elements in plant genomes and have validated the crucial role of repeats in genome structure, function, and evolution (Wicker et al, 2007 ; Shatskikh et al, 2020 ). Once notoriously labeled as “junk DNA,” repetitive elements are now known as important players in gene regulation, stress response, and genome stability (Fedoroff, 2012 ).…”

Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

“…Regardless of the common satDNA composition, centromeric and pericentromeric chromatin are structurally different, essentially because centromeres are epigenetically compatible with kinetochore assembly and chromosome segregation, while pericentromeric regions have a typical heterochromatic behavior [ 26 ]. Thus, the ubiquitous centromeric presence of α satellite sequences is contrasted by the nature of pericentromeric satellite families that clearly behave in a more non-homogenous manner [ 23 , 29 , 55 ], frequently leading to incongruences about their overall existence and location in the human genome [ 95 ].…”

“…Highly repetitive satellite DNA undoubtedly represents a major gap in human genome assemblies, significantly contributing to the lack of high-resolution sequencing studies in the field of centromere genomics, whose characterization has been substantially hindered by the repetitive nature of satDNA [ 26 , 110 , 111 ]. The availability of computer software algorithms for sequence analysis has been highly restricted to methods excluding repetitive sequences and disregarding their annotation [ 6 , 97 , 111 ].…”

“…Given that a wide variety of satellite repeats can be transcribed in noncoding RNAs (ncRNAs), RNA sequencing (RNA-seq) has also become a part of satellite DNA research. Satellite DNA expression may depend on time, tissue, developmental state, or stress conditions [ 18 , 20 , 26 ], clearly making RNA-seq studies noteworthy and subject to constant evolution. In this matter, it is important to emphasize on the different methodological constrains of analyzing small or long ncRNAs.…”

“…We now know that a variety of vital cellular processes is influenced by satDNA arrays: cell cycle, gene expression, or even genome stability [ 26 ]. Being a constitutive element of key structures such as centromeres or telomeres, satDNA has been phenotypically associated with chromosome and cell function in multiple species, specifically in humans [ 27 , 28 ], in which several satDNA families have been progressively identified and characterized, albeit not at the same pace.…”