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: 15.26). 01/2009; 72(4):686-727. DOI: 10.1128/MMBR.00011-08
Source: PubMed

ABSTRACT 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.

1 Follower
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features.
    Frontiers in Bioengineering and Biotechnology 01/2015; 3:31. DOI:10.3389/fbioe.2015.00031
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process.
    PLoS ONE 10(3):e0120732. DOI:10.1371/journal.pone.0120732 · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Genetic structure of two populations of Spirlin, Alburnoides eichwaldii from Karganrud and Chalous Rivers was investigated using six microsatellite molecular markers (CtoF-172، BL1-2b، CnaB-030، LleA-071، Ca3 and Z21908) on 30 individuals from each river. The mean of observed alleles at each locus was 6.5. Allele sizes at CtoF-172, BL1-2b, CnaB-030, LleA-071, Ca3 and Z21908 loci were ranged from 107-147, 147-184, 124-157, 332-387 300-347 and 147-183 bps respectively. Z21908 and Ca3 showed the lowest and highest polymorphism respectively. All loci in both rivers showed deviation from Hardy-Weinberg equilibrium. The number of effective alleles, expected heterozygosity, observed heterozygosity and polymorphism information content (PIC) were 4.86, 0.81, 0.96 and 0.94 respectively confirming the high level of genetic diversity in both populations. The mean FIS value for all loci in both station ranged from -0.23 to -0.30 indicating low possibility for inbreeding occurrence. The analysis of molecular variance (AMOVA) indicated that the percent of variance among and within populations were 6.31 and 93.69 % respectively. The genetic distance was 0.363. Significant FST value (0.063) was observed between two populations. The high level of genetic differentiation may reflect local segregation of two populations because of differences in ecological conditions of two rivers.

Full-text (2 Sources)

Available from
Jan 23, 2015