Satellite DNA: An Evolving Topic

Abstract

Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

Keywords: Next-Generation Sequencing (NGS); centromere; heterochromatin; high-throughput in silico analysis; satellite DNA; satellite DNA evolution; satellite DNA function; satellite DNA transcription; telomere.

Figure 1

(A) After electrophoresis of restriction digested genomic DNA, a distinct prominent band (arrow) against the background smear might be unveiled apparent which contains single fragments corresponding to the individual monomeric members of a satellite DNA (satDNA) family. (B) Southern blot hybridization patterns using satDNA probes against genomic DNA digested with different restriction enzymes. The occurrence of a restriction site for a particular enzyme leads to the complete digestion of an array which leads to a band of monomeric units (type A digestion, [53,61]). However, it is common that part of the array remains as a ‘ladder’ of oligomers of the repeat unit since some units have lost the restriction site by mutation (a, b, c, d, e). On the contrary, mutation may lead to the appearance of occasional restriction sites in some repeats within the array, which is observed as a type B digestion (f, g, h) [53,61]. Patterns of undigested satDNA are found in lines i, j. (C). Ladder-like patterns of satDNA amplification by polymerase chain reaction (PCR). (D). Examples of repeat clusters of satDNA visualized in the form of graphs where nodes represent sequence reads and edges connect reads with sequence similarities as obtained using RepeatExplorer [74,75].

Figure 2

Fluorescent in situ hybridization (FISH) using satDNA probes. Probes were labeled with digoxigenin-dUTP and detected with antidigoxigenin FITC-conjugate. FITC (Fluorescein IsoTioCyanate) is a fluorochrome derivative of fluorescein which fluoresces yellowish-green. In these pictures, yellowish-green signals correspond to detected probes while chromosomes are counterstained with ethidium propide (red). (A) EcoRI satDNA is the main component of the centromeres of the chromosomes of the fish species of the Sparidae family. This picture shows the detection of the hybridization signals of EcoRI repeats on the centromeres of all the chromosomes of Diplodus bellotti [30]. (B) DraI satDNA is located in the subtelomeric region of the chromosomes of some sparid species [29]. This picture shows the detection of the hybridization signals of DraI repeats at the subtelomeric region of many of the chromosomes of Pagrus auriga. The chromosomes of this species are all acrocentric. Also look for the presence of some interstitial loci in some of its chromosomes. (C) RAE180 satDNA is highly amplified in the Y chromosomes of males (XY₁Y₂) of the dioecius plant species Rumex acetosa [25,26,28]. This picture shows the detection of the hybridization signals of RAE180 repeats which are widespread in the major part of the two Y chromosomes. Sex chromosomes are indicated.