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Repetitive DNA Sequences in Eukaryotic Genomes

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 53425

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Special Issue Editors

Prof. Dr. Miroslav Plohl

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Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: repetitive DNA sequences; satellite DNAs; mobile elements; heterochromatin; centromere; telomere; satellitome; evolution of repetitive sequences
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Dr. Eva Šatović-Vukšić

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Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: repetitive DNA sequences; satellite DNA; transposable elements; heterochromatin; NGS; satellitome; repeatome; genome biology; genome evolution, bivalves, insects
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Prof. Dr. Raquel Chaves

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1. CytoGenomics Lab, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
2. BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
Interests: repetitive DNA sequences; satellite DNA; mobile elements; centromere; telomere; satellitome; evolution of repetitive sequences; genome architecture; chromosome restructuring; repetitive DNA transcription; cancer and repetitive sequences
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A large fraction of every eukaryotic genome is composed of noncoding DNA sequences existing in many copies. These sequences were shown to have many important biological functions, for example in defining the entire genome landscape, building centromeres and telomeres, participating in genome rearrangements, modulating gene expression, and being essential in genome resilience and evolution. Regions enriched in repetitive sequences still challenge the understanding of genome structure, because of difficulties in sequence alignments and assemblies of such segments. Rapidly developing sequencing technologies, accessibility to datasets, and novel bioinformatics strategies opened a new era in the research of these mysterious genome components. Combining low-coverage short-read DNA sequencing and specialized bioinformatic tools yields complete repeatome and satellitome data, while technologies enabling long reads from a single molecule determine the precise sequential order of tandem repeats in long arrays. Cytogenetic experiments also add valuable results in studying repetitive DNA sequences on a chromosomal level. Additionally, phylogenetic approaches make possible tracing their evolutionary history in many organisms, as these sequences present astonishing preservation throughout long evolutionary periods. Novel approaches combined with the classical studies lead to better understanding of a genome/chromosome structure and evolution, and open possibilities for additional functional studies of the roles of repetitive sequences. This Special Issue is devoted to promoting the interest of scientific community in the research of this important segment of genome biology.

Prof. Dr. Miroslav Plohl
Dr. Eva Šatović
Prof. Dr. Raquel Chaves
Guest Editors

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Keywords

repetitive DNA sequences
satellite DNA
mobile elements
heterochromatin
centromere
NGS
PacBio
satellitome
repeatome
cytogenetics
phylogenetics
genome biology
genome evolution

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Published Papers (9 papers)

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Research

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19 pages, 3249 KiB

Open AccessArticle

Telomeric-Like Repeats Flanked by Sequences Retrotranscribed from the Telomerase RNA Inserted at DNA Double-Strand Break Sites during Vertebrate Genome Evolution

by Lorenzo Sola, Solomon G. Nergadze, Eleonora Cappelletti, Francesca M. Piras, Elena Giulotto and Marco Santagostino

Int. J. Mol. Sci. 2021, 22(20), 11048; https://doi.org/10.3390/ijms222011048 - 13 Oct 2021

Cited by 2 | Viewed by 2825

Abstract

Interstitial telomeric sequences (ITSs) are stretches of telomeric-like repeats located at internal chromosomal sites. We previously demonstrated that ITSs have been inserted during the repair of DNA double-strand breaks in the course of evolution and that some rodent ITSs, called TERC-ITSs, are flanked by fragments retrotranscribed from the telomerase RNA component (TERC). In this work, we carried out an extensive search of TERC-ITSs in 30 vertebrate genomes and identified 41 such loci in 22 species, including in humans and other primates. The fragment retrotranscribed from the TERC RNA varies in different lineages and its sequence seems to be related to the organization of TERC. Through comparative analysis of TERC-ITSs with orthologous empty loci, we demonstrated that, at each locus, the TERC-like sequence and the ITS have been inserted in one step in the course of evolution. Our findings suggest that telomerase participated in a peculiar pathway of DNA double-strand break repair involving retrotranscription of its RNA component and that this mechanism may be active in all vertebrate species. These results add new evidence to the hypothesis that RNA-templated DNA repair mechanisms are active in vertebrate cells. Full article

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

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21 pages, 2177 KiB

Open AccessArticle

Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome

by Monika Tunjić-Cvitanić, Juan J. Pasantes, Daniel García-Souto, Tonči Cvitanić, Miroslav Plohl and Eva Šatović-Vukšić

Int. J. Mol. Sci. 2021, 22(13), 6798; https://doi.org/10.3390/ijms22136798 - 24 Jun 2021

Cited by 14 | Viewed by 3460

Abstract

Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level. Full article

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

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18 pages, 8353 KiB

Open AccessArticle

Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species

by Eugenia E. Montiel, Francisco Panzera, Teresa Palomeque, Pedro Lorite and Sebastián Pita

Int. J. Mol. Sci. 2021, 22(11), 6052; https://doi.org/10.3390/ijms22116052 - 3 Jun 2021

Cited by 25 | Viewed by 3467

Abstract

The triatomine Rhodnius prolixus is the main vector of Chagas disease in countries such as Colombia and Venezuela, and the first kissing bug whose genome has been sequenced and assembled. In the repetitive genome fraction (repeatome) of this species, the transposable elements represented 19% of R. prolixus genome, being mostly DNA transposon (Class II elements). However, scarce information has been published regarding another important repeated DNA fraction, the satellite DNA (satDNA), or satellitome. Here, we offer, for the first time, extended data about satellite DNA families in the R. prolixus genome using bioinformatics pipeline based on low-coverage sequencing data. The satellitome of R. prolixus represents 8% of the total genome and it is composed by 39 satDNA families, including four satDNA families that are shared with Triatoma infestans, as well as telomeric (TTAGG)_n and (GATA)_n repeats, also present in the T. infestans genome. Only three of them exceed 1% of the genome. Chromosomal hybridization with these satDNA probes showed dispersed signals over the euchromatin of all chromosomes, both in autosomes and sex chromosomes. Moreover, clustering analysis revealed that most abundant satDNA families configured several superclusters, indicating that R. prolixus satellitome is complex and that the four most abundant satDNA families are composed by different subfamilies. Additionally, transcription of satDNA families was analyzed in different tissues, showing that 33 out of 39 satDNA families are transcribed in four different patterns of expression across samples. Full article

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

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14 pages, 1783 KiB

Open AccessArticle

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

by Juan A. Subirana and Xavier Messeguer

Int. J. Mol. Sci. 2021, 22(10), 5373; https://doi.org/10.3390/ijms22105373 - 20 May 2021

Cited by 3 | Viewed by 2527

Abstract

Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies. Full article

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

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12 pages, 2314 KiB

Open AccessArticle

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

by Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen and Neil D. Young

Int. J. Mol. Sci. 2021, 22(4), 1811; https://doi.org/10.3390/ijms22041811 - 11 Feb 2021

Cited by 22 | Viewed by 5386

Abstract

Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow. Full article

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

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16 pages, 2996 KiB

Open AccessArticle

Distinct Regulation of the Expression of Satellite DNAs in the Beetle Tribolium castaneum

by Antonio Sermek, Isidoro Feliciello and Đurđica Ugarković

Int. J. Mol. Sci. 2021, 22(1), 296; https://doi.org/10.3390/ijms22010296 - 30 Dec 2020

Cited by 7 | Viewed by 2584

Abstract

In the flour beetle, Tribolium castaneum (peri)centromeric heterochromatin is mainly composed of a major satellite DNA TCAST1 interspersed with minor satellites. With the exception of heterochromatin, clustered satellite repeats are found dispersed within euchromatin. In order to uncover a possible satellite DNA function within the beetle genome, we analysed the expression of the major TCAST1 and a minor TCAST2 satellite during the development and upon heat stress. The results reveal that TCAST1 transcription was strongly induced at specific embryonic stages and upon heat stress, while TCAST2 transcription is stable during both processes. TCAST1 transcripts are processed preferentially into piRNAs during embryogenesis and into siRNAs during later development, contrary to TCAST2 transcripts, which are processed exclusively into piRNAs. In addition, increased TCAST1 expression upon heat stress is accompanied by the enrichment of the silent histone mark H3K9me3 on the major satellite, while the H3K9me3 level at TCAST2 remains unchanged. The transcription of the two satellites is proposed to be affected by the chromatin state: heterochromatin and euchromatin, which are assumed to be the prevalent sources of TCAST1 and TCAST2 transcripts, respectively. In addition, distinct regulation of the expression might be related to diverse roles that major and minor satellite RNAs play during the development and stress response. Full article

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

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Review

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20 pages, 1366 KiB

Open AccessReview

Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

by Mariana Lopes, Sandra Louzada, Margarida Gama-Carvalho and Raquel Chaves

Int. J. Mol. Sci. 2021, 22(9), 4707; https://doi.org/10.3390/ijms22094707 - 29 Apr 2021

Cited by 8 | Viewed by 4987

Abstract

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology. Full article

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

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28 pages, 1150 KiB

Open AccessReview

Sequence, Chromatin and Evolution of Satellite DNA

by Jitendra Thakur, Jenika Packiaraj and Steven Henikoff

Int. J. Mol. Sci. 2021, 22(9), 4309; https://doi.org/10.3390/ijms22094309 - 21 Apr 2021

Cited by 121 | Viewed by 20855

Abstract

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals. Full article

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

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10 pages, 431 KiB

Open AccessReview

Repetitive Elements in Humans

by Thomas Liehr

Int. J. Mol. Sci. 2021, 22(4), 2072; https://doi.org/10.3390/ijms22042072 - 19 Feb 2021

Cited by 30 | Viewed by 4714

Abstract

Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well. Full article

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

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