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Biomolecules
Special Issues
The Evolution and Function of Repetitive DNA
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The Evolution and Function of Repetitive DNA

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 2512

Special Issue Editors

Prof. Dr. Raquel Chaves

E-Mail Website
Guest Editor
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
Dr. Sandra Louzada

E-Mail Website
Guest Editor
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: satellite DNA; satellite DNA evolution; karyotype restructuring; human pericentromeric sequences; satellite non-coding RNA; chromosome rearrangements

Special Issue Information

Dear Colleagues,

Repetitive DNA has long been one of the most intriguing but also overlooked portions of eukaryotic genomes. This class of DNA encompasses sequences either organized in a tandem fashion (including satellite DNA) or dispersed in the genome (transposable elements). Repetitive DNA can be highly variable between species in terms of sequence, abundance, and chromosome location. This results from their astonishing ability to change in short evolutionary periods due to the fast-evolving nature of DNA. Moreover, their dynamic behavior may also contribute to genome remodeling by accompanying the rearrangements.

These sequences can build up important structures such as telomeres and centromeres, which are responsible for the proper chromosome segregation, and have been implicated in numerous important functions in the genome. The ability of repetitive sequences to originate non-coding RNA transcripts, which are associated with regulatory and structural functions, has constituted a turnover point. For instance, satellite non-coding RNAs and transposable elements deregulation have been associated to cancer, autoimmune, developmental and degenerative diseases. There is still a long way to go for the knowledge of repetitive DNA function to match that of the coding sequences, and their repetitive nature still poses some technical issues. However, the available genomic technologies and the continuation of the development of new methodologies is potentiating the study of these sequences in the genome of different species.

We kindly invite the submission of manuscripts covering these topics, exploring the role of the transcription of repetitive DNA and the significance of its deregulation in the genome, the hindering of the evolution mechanisms that shape these sequences and their contribution in remodeling genomes.

Prof. Dr. Raquel Chaves
Dr. Sandra Louzada
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • repetitive DNA
  • satellite DNA
  • transposable elements
  • non-coding RNA transcripts
  • evolution of repetitive DNA
  • genome instability
  • genome evolution

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Published Papers (2 papers)

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Research

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13 pages, 2757 KiB  
Article
Evolutionary Dynamics of Satellite DNA Repeats across the Tettigoniidae Family: Insights from Genomic Analysis
by Muhammad Majid, Hashim Khan, Xuanzeng Liu, Muhammad Shaheer and Yuan Huang
Biomolecules 2024, 14(8), 915; https://doi.org/10.3390/biom14080915 - 27 Jul 2024
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Abstract
Satellite DNA repeats are repetitive DNA sequences found in eukaryotic genomes, typically consisting of short DNA motifs repeated in tandem arrays. Despite the vast body of literature on satellite DNA repeats in other taxa, investigations specifically targeting Tettigoniidae remain conspicuously absent. Our study [...] Read more.
Satellite DNA repeats are repetitive DNA sequences found in eukaryotic genomes, typically consisting of short DNA motifs repeated in tandem arrays. Despite the vast body of literature on satellite DNA repeats in other taxa, investigations specifically targeting Tettigoniidae remain conspicuously absent. Our study aims to fill a critical gap in our understanding of satellitome evolutionary processes shaping Tettigoniidae genomes. Repeatome analysis revealed that the Meconema thalassinum genome comprises 92%, and Phryganogryllacris superangulata had the lowest value of 34%, with an average of 67% in other Tettigoniidae species. The analysis reveals significant variation in the number of satellite DNA repeats across species of the Tettigoniidae family, with M. thalassinum exhibiting the highest count, 246, reported in insects to date and the lowest count, 10, in Pholidoptera griseoptera. Ruspolia dubia and Ruspolia yunnana, which are congeneric species, showcase distinct counts of 104 and 84 families, respectively. Satellite DNA repeats in R. dubia exhibit the highest abundance, constituting 17.2% of the total genome, while the lowest abundance was reported in P. griseoptera, at 5.65%. The genome size correlates weakly with the satellite DNA family count (rs = 0.42, p = 0.29), but a strong correlation exists between satellite abundance and family number (rs = 0.73, p = 0.03). Moreover, the analysis of satellite DNA gain and loss patterns provides insights into the amplification and homogenization of satellite DNA families within the genome, with species-specific repeats exhibiting a positive trend toward amplification. The chromosomal distribution in M. thalassinum displayed that the highest accumulation was observed on Chr12, Chr01, and Chr04, constituting 17.79%, 17.4%, and 17.22% of the total chromosome size, respectively. The chromosome-specific propagation of satellite DNA families was evident, with MthSat01 solely on chromosome 1 and MthSat170 on chromosome 2, sharing 1.64% and 2.33%. The observed conservation and variations in satellite DNA number and abundances, along with distinct patterns of gain and loss, indicate the influence of potentially diverse evolutionary processes shaping the genomic landscape of these insects, which requires further investigation. Furthermore, the differential accumulation of satellite DNA on specific chromosomes implies that potential chromosome-specific functions or structural features influence the retention and proliferation of satellite sequences. Full article
(This article belongs to the Special Issue The Evolution and Function of Repetitive DNA)
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Review

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14 pages, 968 KiB  
Review
Answering the Cell Stress Call: Satellite Non-Coding Transcription as a Response Mechanism
by Marisa Fonseca-Carvalho, Gabriela Veríssimo, Mariana Lopes, Daniela Ferreira, Sandra Louzada and Raquel Chaves
Biomolecules 2024, 14(1), 124; https://doi.org/10.3390/biom14010124 - 17 Jan 2024
Cited by 1 | Viewed by 1604
Abstract
Organisms are often subjected to conditions that promote cellular stress. Cell responses to stress include the activation of pathways to defend against and recover from the stress, or the initiation of programmed cell death to eliminate the damaged cells. One of the processes [...] Read more.
Organisms are often subjected to conditions that promote cellular stress. Cell responses to stress include the activation of pathways to defend against and recover from the stress, or the initiation of programmed cell death to eliminate the damaged cells. One of the processes that can be triggered under stress is the transcription and variation in the number of copies of satellite DNA sequences (satDNA), which are involved in response mechanisms. Satellite DNAs are highly repetitive tandem sequences, mainly located in the centromeric and pericentromeric regions of eukaryotic chromosomes, where they form the constitutive heterochromatin. Satellite non-coding RNAs (satncRNAs) are important regulators of cell processes, and their deregulation has been associated with disease. Also, these transcripts have been associated with stress-response mechanisms in varied eukaryotic species. This review intends to explore the role of satncRNAs when cells are subjected to adverse conditions. Studying satDNA transcription under various stress conditions and deepening our understanding of where and how these sequences are involved could be a key factor in uncovering important facts about the functions of these sequences. Full article
(This article belongs to the Special Issue The Evolution and Function of Repetitive DNA)
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