Shapiro, JA and von Sternberg, R. Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc 80: 227-250

Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
Biological Reviews (Impact Factor: 9.67). 06/2005; 80(2):227-50. DOI: 10.1017/S1464793104006657
Source: PubMed


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 plays various roles in genomes ranging from genome organization, centromere assembly, telomere formation and related aging process, epigenetic modulation of associated loci, rapid genetic variation in times of stress and adaptive immune system in vertebrates and possibly speciation2021. Repetitive DNAs were also involved in human diseases. For example, expansion of intragenic triplet repeats in humans is associated with various diseases, including Huntington chorea, myotonic dystrophy, synpolydactyly and fragile X syndrome222324252627. Therefore repetitive sequences are of evolutionary, biological, biotechnological and medical significance and cannot be ignored17. "
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    ABSTRACT: Designer transcription-activator like effectors (TALEs) is a promising technology and made it possible to edit genomes with higher specificity. Such specific engineering and gene regulation technologies are also being developed using RNA-binding proteins like PUFs and PPRs. The main feature of TALEs, PUFs and PPRs is their repetitive DNA/RNA-binding domains which have single nucleotide binding specificity. Available kits today allow researchers to assemble these repetitive domains in any combination they desire when generating TALEs for gene targeting and editing. However, PCR amplifications of such repetitive DNAs are highly problematic as these mostly fail, generating undesired artifact products or deletions. Here we describe the molecular mechanisms leading to these artifacts. We tested our models also in plasmid templates containing one copy versus two copies of GFP-coding sequence arranged as either direct or inverted repeats. Some limited solutions in amplifying repetitive DNA regions are described.
    Scientific Reports 05/2014; 4(Article number: 5052). DOI:10.1038/srep05052 · 5.58 Impact Factor
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