Special Issue "Repetitive DNA Sequences"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 January 2019)

Special Issue Editors

Guest Editor
Prof. Andrew G. Clark

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Interests: Drosophila; genetic variation; natural populations; quantitative modeling of phenotypes; genomics;
Guest Editor
Prof. Daniel A. Barbash

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Interests: heterochromatic DNA; non-coding regulatory DNA; Drosophila; transposable elements; satellite DNA
Guest Editor
Dr. Sarah E. Lower

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Interests: repetitive DNA evolution; Drosophila; Fireflies; satellite DNA; genome sequencing;
Guest Editor
Dr. Anne-Marie Dion-Côté

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA and Department of Ecology and Genetics Evolutionsbiologiskt Centrum, Uppsala University, Uppsala, Sweden.
Website | E-Mail
Interests: satellite DNA; genomics; mutation; transcriptomics; epigenetics; next generation sequencing;

Special Issue Information

Dear Colleagues,

Repetitive DNAs are ubiquitous in eukaryotic genomes, and, in many species, comprise the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNAs are often ignored in genomic studies, due to technical challenges in identifying, assembling and quantifying them. New technologies and methods are now allowing unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNAs are of particular interest because they can represent distinct modes of genome evolution. Some repetitive DNAs form essential genome structures, such as telomeres and centromeres, that are required for proper chromosome maintenance and segregation, while others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and cause genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. Yet even these “neutral” repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.

Prof. Andrew G. Clark
Prof. Daniel A. Barbash
Dr. Sarah E. Lower
Dr. Anne-Marie Dion-Côté
Guest Editors

Manuscript Submission Information

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Keywords

  • repetitive DNA
  • transposable element
  • heterochromatin
  • genome evolution
  • genomic conflict

Published Papers (4 papers)

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Research

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Open AccessArticle The Integrity of piRNA Clusters is Abolished by Insulators in the Drosophila Germline
Received: 29 January 2019 / Revised: 27 February 2019 / Accepted: 6 March 2019 / Published: 11 March 2019
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Abstract
Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure [...] Read more.
Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the retrotransposon gypsy. To understand how insulators contribute to piRNA cluster activity, we studied the effects of transgenes containing gypsy insulators on local organization of endogenous piRNA clusters. We show that transgene insertions interfere with piRNA precursor transcription, small RNA production and the formation of piRNA cluster-specific chromatin, a hallmark of which is Rhino, the germline homolog of the heterochromatin protein 1 (HP1). The mutations of Su(Hw) restored the integrity of piRNA clusters in transgenic strains. Surprisingly, Su(Hw) depletion enhanced the production of piRNAs by the domesticated telomeric retrotransposon TART, indicating that Su(Hw)-dependent elements protect TART transcripts from piRNA processing machinery in telomeres. A genome-wide analysis revealed that Su(Hw)-binding sites are depleted in endogenous germline piRNA clusters, suggesting that their functional integrity is under strict evolutionary constraints. Full article
(This article belongs to the Special Issue Repetitive DNA Sequences)
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Open AccessArticle Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups
Received: 21 January 2019 / Revised: 13 February 2019 / Accepted: 15 February 2019 / Published: 20 February 2019
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Abstract
Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken [...] Read more.
Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population. Full article
(This article belongs to the Special Issue Repetitive DNA Sequences)
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Review

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Open AccessReview Centromere Repeats: Hidden Gems of the Genome
Received: 8 February 2019 / Revised: 7 March 2019 / Accepted: 11 March 2019 / Published: 16 March 2019
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Abstract
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the [...] Read more.
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’. Full article
(This article belongs to the Special Issue Repetitive DNA Sequences)
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Open AccessReview Sequence Expression of Supernumerary B Chromosomes: Function or Fluff?
Received: 16 January 2019 / Revised: 1 February 2019 / Accepted: 5 February 2019 / Published: 8 February 2019
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Abstract
B chromosomes are enigmatic heritable elements found in the genomes of numerous plant and animal species. Contrary to their broad distribution, most B chromosomes are non-essential. For this reason, they are regarded as genome parasites. In order to be stably transmitted through generations, [...] Read more.
B chromosomes are enigmatic heritable elements found in the genomes of numerous plant and animal species. Contrary to their broad distribution, most B chromosomes are non-essential. For this reason, they are regarded as genome parasites. In order to be stably transmitted through generations, many B chromosomes exhibit the ability to “drive”, i.e., they transmit themselves at super-Mendelian frequencies to progeny through directed interactions with the cell division apparatus. To date, very little is understood mechanistically about how B chromosomes drive, although a likely scenario is that expression of B chromosome sequences plays a role. Here, we highlight a handful of previously identified B chromosome sequences, many of which are repetitive and non-coding in nature, that have been shown to be expressed at the transcriptional level. We speculate on how each type of expressed sequence could participate in B chromosome drive based on known functions of RNA in general chromatin- and chromosome-related processes. We also raise some challenges to functionally testing these possible roles, a goal that will be required to more fully understand whether and how B chromosomes interact with components of the cell for drive and transmission. Full article
(This article belongs to the Special Issue Repetitive DNA Sequences)
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