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Shapiro JA, von Sternberg R.. Why repetitive DNA is essential to genome function. Biol Rev 80: 1-24

Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
Biological Reviews (Impact Factor: 9.79). 06/2005; 80(2):227-50. DOI: 10.1017/S1464793104006657
Source: PubMed

ABSTRACT There are clear theoretical reasons and many well-documented examples which show that repetitive, DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.

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Available from: James Shapiro, Jan 29, 2015
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    • "Regions of approximate tandem repeats in genomes are abundant in many species from bacteria to mammals, and are essential for many structures and functions of genomes (Shapiro and Sternberg, 2005). For example, many researchers revealed that the 3-periodicity of a DNA sequence indicates protein coding regions and it is used for protein coding region identication (Silverman and Linsker, 1986; Tiwari et al., 1997). "
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    ABSTRACT: Latent periodic elements in genomes play important roles in genomic functions. Many complex periodic elements in genomes are difficult to be detected by commonly used digital signal processing (DSP). We present a novel method to compute the periodic power spectrum of a DNA sequence based on the nucleotide distributions on periodic positions of the sequence. The method directly calculates full periodic spectrum of a DNA sequence rather than frequency spectrum by Fourier transform. The magnitude of the periodic power spectrum reflects the strength of the periodicity signals, thus, the algorithm can capture all the latent periodicities in DNA sequences. We apply this method on detection of latent periodicities in different genome elements, including exons and microsatellite DNA sequences. The results show that the method minimizes the impact of spectral leakage, captures a much broader latent periodicities in genomes, and outperforms the conventional Fourier transform.
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    • "Grewal and Elgin [56] proposed the transcription of satDNA and its impact on heterochromatin, particularly in terms of the formation and maintenance of heterochromatin structure. Repetitive DNA sequence elements are also involved in cooperative molecular interactions for the formation of nucleoprotein complexes [57]. Repeat sequences may attract some specific nuclear proteins, and the chromatin folding code dictates the DNA–protein interactions, which may underlie the genetic function of the tandem repeats [58]. "
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    ABSTRACT: Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150–400 base pairs (bp) in length. Repetitive sequences may be species- or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as “tuning knobs” in evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing technology, it is possible to evaluate complex genomes for analyzing repetitive sequences and deciphering the yet unknown functional potential of repetitive sequences.
    Genomics Proteomics & Bioinformatics 08/2014; 12(4). DOI:10.1016/j.gpb.2014.07.003
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    • "Repetitive DNA sequences are convenient for the studies of the genome evolution [11] [12] [13]. According to Ohno [14], this fraction originates in the process of gene duplications and has a potential for large-scale rearrangements, because they are not subjected to the pressing of the natural selection. "
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    ABSTRACT: The aim of the study is a comparative investigation of changes that certain genome parts undergo during speciation. The research was focused on divergence of coding and noncoding sequences in different groups of salmonid fishes of the Salmonidae (Salmo, Parasalmo, Oncorhynchus, and Salvelinus genera) and the Coregonidae families under different levels of reproductive isolation. Two basic approaches were used: (1) PCR-RAPD with a 20-22 nt primer design with subsequent cloning and sequencing of the products and (2) a modified endonuclease restriction analysis. The restriction fragments were shown with sequencing to represent satellite DNA. Effects of speciation are found in repetitive sequences. The revelation of expressed sequences in the majority of the employed anonymous loci allows for assuming the adaptive selection during allopatric speciation in isolated char forms.
    07/2013; 2013:629543. DOI:10.1155/2013/629543
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