Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
Microbiology and molecular biology reviews: MMBR (Impact Factor: 14.61). 01/2009; 72(4):686-727. DOI: 10.1128/MMBR.00011-08
Source: PubMed


Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

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Available from: Guy-Franck Richard, Jan 23, 2015
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    • "The low density of microsatellites in general may explain the low numbers of microsatellites with many repeats. Microsatellites in fungi could possibly be affected by fungal life cycles, as many fungi are predominantly haploid and asexual with occasional diploid, sexual stages, and mutations of microsatellites may occur during meiosis (Richard et al. 2008); however, the lack of sexual recombination does not appear to affect microsatellite evolution (Kayser et al. 2000; Paun and Hörandl 2006; Weetman et al. 2006). Because of the challenges with analyzing microsatellite data, many authors have begun using single nucleotide polymorphisms (SNPs) found in the regions flanking microsatellites as additional genetic markers (Barthe et al. 2012; Payseur and Jing 2009). "
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    ABSTRACT: The evolution of nine microsatellites and one minisatellite was investigated in the fungus Fusarium oxysporum and sister taxa Fusarium redolens and Fusarium verticillioides. Compared to other organisms, fungi have been reported to contain fewer and less polymorphic microsatellites. Mutational patterns over evolutionary time were studied for these ten loci by mapping changes in core repeat numbers onto a phylogeny based on the sequence of the conserved translation elongation factor 1-α gene. The patterns of microsatellite formation, expansion, and interruption by base substitutions were followed across the phylogeny, showing that these loci are evolving in a manner similar to that of microsatellites in other eukaryotes. Most mutations could be fit to a stepwise mutation model, but a few appear to have involved multiple repeat units. No evidence of gene conversion was seen at the minisatellite locus, which may also be mutating by replication slippage. Some homoplastic numbers of repeat units were observed for these loci, and polymorphisms in the regions flanking the microsatellites may provide better genetic markers for population genetics studies of these species.
    Full-text · Article · Dec 2015 · Journal of Molecular Evolution
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    • "Despite initially considered useless genomic elements (Ohno 1972), the repetitive sequences are presently seen as an important fraction of the eukaryotic genome to which several functions have been ascribed (e.g., Richard et al. 2008; Hall et al. 2012; Rebollo et al. 2012; Enukashvily and Ponomartsev 2013; Plohl et al. 2014). Emerging contribution to centromere structure and function have been indicated as one of the main roles of (peri)centromeric satDNAs, which could be associated with kinetochore formation, spindle microtubule attachment, and sister chromatid cohesion (e.g., Guenatri et al. 2004; Wong et al. 2007; Hall et al. 2012; Enukashvily and Ponomartsev 2013; Plohl et al. 2014). "
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    DESCRIPTION: Three novel repetitive DNA sequences are described, presenting a similar heterochromatic chromosomal location in two hamster species: Phodopus roborovskii and Phodopus sungorus (Cricetidae, Rodentia). Namely, two species-specific repetitive sequences (PROsat from P. roborovskii and PSUchr1sat from P. sungorus) surrounding a third one (PsatDNA), that is shared by both hamster genomes. Fiber-FISH analyses revealed that PROsat intermingles with PsatDNA in P. roborovskii and PSUchr1sat intermingles with PsatDNA in P. sungorus. A model explaining the evolution of this intricate chromosomal distribution is proposed, which can explain better the evolution of these very derivative genomes (in comparison to the ancestral Muroidea). The most plausible evolutionary scenario seems to be the expansion of a number of repeats into other’s domain, most probably resulting in its intermingling, followed by the subsequent spread of these complex repeats from a single chromosomal location to other chromosomes. Evidences of an association between repetitive sequences and the chromosome evolution process were observed, namely for PROsat. Most probably, the evolutionary breakpoints that shaped PRO and PSU chromosomes (pericentric inversions and fusions) occurred within the boundaries of PROsat blocks in the ancestor. The repeats high diversity at the heterochromatic regions of Phodopus chromosomes, together with its complex organization, suggests that these species are important models for evolutionary studies, namely in the investigation of a possible relationship between repetitive sequences and the occurrence of chromosomal rearrangements and consequently, in genome evolution.
    Full-text · Research · Nov 2015
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    • "On one side, metagenomic assemblies of complex eukaryotic genomes are challenging due to the occurrence of repeat DNA regions (Richard et al., 2008) that cannot be overcome with most sequencing technologies. This technological limitation might affect the effective assembly of P. antarctica and diatom genomes directly from bloom events. "
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    ABSTRACT: Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.
    Full-text · Article · Oct 2015 · Frontiers in Microbiology
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