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Repetitive DNA Sequences

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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) | Viewed by 76134

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Special Issue Editors

Prof. Andrew G. Clark

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Guest Editor

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
Interests: Drosophila; genetic variation; natural populations; quantitative modeling of phenotypes; genomics;

Prof. Daniel A. Barbash

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Guest Editor

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
Interests: heterochromatic DNA; non-coding regulatory DNA; Drosophila; transposable elements; satellite DNA

Dr. Sarah E. Lower

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Guest Editor

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
Interests: repetitive DNA evolution; Drosophila; fireflies; satellite DNA; genome sequencing;

Assist. Prof. Anne-Marie Dion-Côté

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Guest Editor

Biology department, Université de Moncton, Moncton, NB, Canada
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

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Keywords

repetitive DNA
transposable element
heterochromatin
genome evolution
genomic conflict

Published Papers (12 papers)

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Editorial

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3 pages, 176 KiB

Open AccessEditorial

Special Issue: Repetitive DNA Sequences

by Sarah E. Lower, Anne-Marie Dion-Côté, Andrew G. Clark and Daniel A. Barbash

Genes 2019, 10(11), 896; https://doi.org/10.3390/genes10110896 - 06 Nov 2019

Cited by 7 | Viewed by 3703

Abstract

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. However, 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. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

Research

Jump to: Editorial, Review

23 pages, 4119 KiB

Open AccessArticle

Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution

by Changcheng Wu and Jian Lu

Genes 2019, 10(5), 338; https://doi.org/10.3390/genes10050338 - 06 May 2019

Cited by 26 | Viewed by 6352

Abstract

Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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17 pages, 1921 KiB

Open AccessArticle

The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch

by Jesper Boman, Carolina Frankl-Vilches, Michelly da Silva dos Santos, Edivaldo H. C. de Oliveira, Manfred Gahr and Alexander Suh

Genes 2019, 10(4), 301; https://doi.org/10.3390/genes10040301 - 13 Apr 2019

Cited by 16 | Viewed by 6215

Abstract

Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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19 pages, 1801 KiB

Open AccessArticle

Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

by Romain Lannes, Carène Rizzon and Emmanuelle Lerat

Genes 2019, 10(3), 249; https://doi.org/10.3390/genes10030249 - 26 Mar 2019

Cited by 8 | Viewed by 3269

Abstract

Epigenetic modifications have an important role to explain part of the intra- and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential presence of TEs in the evolutionary divergence of duplicates through variation in the epigenetic landscape. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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14 pages, 1879 KiB

Open AccessArticle

The Integrity of piRNA Clusters is Abolished by Insulators in the Drosophila Germline

by Elizaveta Radion, Olesya Sokolova, Sergei Ryazansky, Pavel A. Komarov, Yuri Abramov and Alla Kalmykova

Genes 2019, 10(3), 209; https://doi.org/10.3390/genes10030209 - 11 Mar 2019

Cited by 6 | Viewed by 4072

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 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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11 pages, 854 KiB

Open AccessArticle

Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups

by Mats E. Pettersson and Patric Jern

Genes 2019, 10(2), 162; https://doi.org/10.3390/genes10020162 - 20 Feb 2019

Cited by 7 | Viewed by 4760

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 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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23 pages, 1979 KiB

Open AccessReview

On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

by Yann Bourgeois and Stéphane Boissinot

Genes 2019, 10(6), 419; https://doi.org/10.3390/genes10060419 - 30 May 2019

Cited by 75 | Viewed by 8437

Abstract

Transposable elements (TEs) play an important role in shaping genomic organization and structure, and may cause dramatic changes in phenotypes. Despite the genetic load they may impose on their host and their importance in microevolutionary processes such as adaptation and speciation, the number of population genetics studies focused on TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review the current knowledge about the dynamics of transposable elements at recent evolutionary time scales, and discuss the mechanisms that condition their abundance and frequency. We first discuss non-adaptive mechanisms such as purifying selection and the variable rates of transposition and elimination, and then focus on positive and balancing selection, to finally conclude on the potential role of TEs in causing genomic incompatibilities and eventually speciation. We also suggest possible ways to better model TEs dynamics in a population genomics context by incorporating recent advances in TEs into the rich information provided by SNPs about the demography, selection, and intrinsic properties of genomes. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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14 pages, 1795 KiB

Open AccessReview

Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population

by Karen H. Miga

Genes 2019, 10(5), 352; https://doi.org/10.3390/genes10050352 - 08 May 2019

Cited by 56 | Viewed by 8335

Abstract

The central goal of medical genomics is to understand the inherited basis of sequence variation that underlies human physiology, evolution, and disease. Functional association studies currently ignore millions of bases that span each centromeric region and acrocentric short arm. These regions are enriched in long arrays of tandem repeats, or satellite DNAs, that are known to vary extensively in copy number and repeat structure in the human population. Satellite sequence variation in the human genome is often so large that it is detected cytogenetically, yet due to the lack of a reference assembly and informatics tools to measure this variability, contemporary high-resolution disease association studies are unable to detect causal variants in these regions. Nevertheless, recently uncovered associations between satellite DNA variation and human disease support that these regions present a substantial and biologically important fraction of human sequence variation. Therefore, there is a pressing and unmet need to detect and incorporate this uncharacterized sequence variation into broad studies of human evolution and medical genomics. Here I discuss the current knowledge of satellite DNA variation in the human genome, focusing on centromeric satellites and their potential implications for disease. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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15 pages, 896 KiB

Open AccessReview

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

by Radka Symonová

Genes 2019, 10(5), 345; https://doi.org/10.3390/genes10050345 - 07 May 2019

Cited by 47 | Viewed by 7946

Abstract

Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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14 pages, 1065 KiB

Open AccessReview

Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

by Justin P. Blumenstiel

Genes 2019, 10(5), 336; https://doi.org/10.3390/genes10050336 - 03 May 2019

Cited by 34 | Viewed by 4982

Abstract

Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts. Full article

(This article belongs to the Special Issue Repetitive DNA Sequences)

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22 pages, 1623 KiB

Open AccessReview

Centromere Repeats: Hidden Gems of the Genome

by Gabrielle Hartley and Rachel J. O’Neill

Genes 2019, 10(3), 223; https://doi.org/10.3390/genes10030223 - 16 Mar 2019

Cited by 87 | Viewed by 12098

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 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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13 pages, 833 KiB

Open AccessReview

Sequence Expression of Supernumerary B Chromosomes: Function or Fluff?

by Elena Dalla Benetta, Omar S. Akbari and Patrick M. Ferree

Genes 2019, 10(2), 123; https://doi.org/10.3390/genes10020123 - 08 Feb 2019

Cited by 22 | Viewed by 4659

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, 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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