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DNA
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DNA Organization in Model Organisms
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DNA Organization in Model Organisms

A special issue of DNA (ISSN 2673-8856).

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 2554

Special Issue Editor

Dr. Alla Grishok

E-Mail Website
Guest Editor
Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
Interests: gene regulation; chromatin organization; enhancers; ncRNA; epigenetics; C. elegans

Special Issue Information

Dear Colleagues,

Our knowledge of genes, their expression regulation, and, later, whole genome organization came from studies of numerous model organisms. They have unique and conserved features, and research of both specialized and common mechanisms utilized by diverse living forms contributes to scientific progress. One recent example is the revolutionary adaptation of the bacterial defense system CRISPR/Cas9 for gene editing.

This Special Issue aims to highlight the latest advances in the genetics and genomics of model organisms, from viruses to vertebrates, including genome and chromatin organization, the evolution of specific genetic and epigenetics features, and new approaches and research tools in genome manipulation.

Dr. Alla Grishok
Guest Editor

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. DNA is an international peer-reviewed open access quarterly 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 1000 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

  • model organism
  • genome
  • chromatin/chromosomes
  • epigenetic inheritance
  • gene editing

Published Papers (4 papers)

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Review

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13 pages, 1002 KiB  
Review
Activity and Silencing of Transposable Elements in C. elegans
by Sylvia E. J. Fischer
DNA 2024, 4(2), 129-140; https://doi.org/10.3390/dna4020007 - 02 Apr 2024
Viewed by 320
Abstract
Since the discovery of transposable elements (TEs) in maize in the 1940s by Barbara McClintock transposable elements have been described as junk, as selfish elements with no benefit to the host, and more recently as major determinants of genome structure and genome evolution. [...] Read more.
Since the discovery of transposable elements (TEs) in maize in the 1940s by Barbara McClintock transposable elements have been described as junk, as selfish elements with no benefit to the host, and more recently as major determinants of genome structure and genome evolution. TEs are DNA sequences that are capable of moving to new sites in the genome and making additional copies of themselves while doing so. To limit the propagation of TEs, host silencing mechanisms are directed at transposon-encoded genes that are required for mobilization. The mutagenic properties of TEs, the potential of TEs to form new genes and affect gene expression, together with the host silencing mechanisms, shape eukaryotic genomes and drive genome evolution. While TEs constitute more than half of the genome in many higher eukaryotes, transposable elements in the nematode C. elegans form a relatively small proportion of the genome (approximately 15%). Genetic studies of transposon silencing, and the discovery of RNA interference (RNAi) in C. elegans, propelled Caenorhabditis elegans (C. elegans) to the forefront of studies of RNA-based mechanisms that silence TEs. Here, I will review the transposable elements that are present and active in the C. elegans genome, and the host defense mechanisms that silence these elements. Full article
(This article belongs to the Special Issue DNA Organization in Model Organisms)
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20 pages, 1764 KiB  
Review
How Chromatin Motor Complexes Influence the Nuclear Architecture: A Review of Chromatin Organization, Cohesins, and Condensins with a Focus on C. elegans
by Bahaar Chawla and Györgyi Csankovszki
DNA 2024, 4(1), 84-103; https://doi.org/10.3390/dna4010005 - 11 Mar 2024
Viewed by 592
Abstract
Chromatin is the complex of DNA and associated proteins found in the nuclei of living organisms. How it is organized is a major research field as it has implications for replication, repair, and gene expression. This review summarizes the current state of the [...] Read more.
Chromatin is the complex of DNA and associated proteins found in the nuclei of living organisms. How it is organized is a major research field as it has implications for replication, repair, and gene expression. This review summarizes the current state of the chromatin organization field, with a special focus on chromatin motor complexes cohesin and condensin. Containing the highly conserved SMC proteins, these complexes are responsible for organizing chromatin during cell division. Additionally, research has demonstrated that condensin and cohesin also have important functions during interphase to shape the organization of chromatin and regulate expression of genes. Using the model organism C. elegans, the authors review the current knowledge of how these complexes perform such diverse roles and what open questions still exist in the field. Full article
(This article belongs to the Special Issue DNA Organization in Model Organisms)
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20 pages, 1247 KiB  
Review
Chromatin Organization during C. elegans Early Development
by Eshna Jash and Györgyi Csankovszki
DNA 2024, 4(1), 64-83; https://doi.org/10.3390/dna4010004 - 22 Feb 2024
Viewed by 560
Abstract
Embryogenesis is characterized by dynamic chromatin remodeling and broad changes in chromosome architecture. These changes in chromatin organization are accompanied by transcriptional changes, which are crucial for the proper development of the embryo. Several independent mechanisms regulate this process of chromatin reorganization, including [...] Read more.
Embryogenesis is characterized by dynamic chromatin remodeling and broad changes in chromosome architecture. These changes in chromatin organization are accompanied by transcriptional changes, which are crucial for the proper development of the embryo. Several independent mechanisms regulate this process of chromatin reorganization, including the segregation of chromatin into heterochromatin and euchromatin, deposition of active and repressive histone modifications, and the formation of 3D chromatin domains such as TADs and LADs. These changes in chromatin structure are directly linked to developmental milestones such as the loss of developmental plasticity and acquisition of terminally differentiated cell identities. In this review, we summarize these processes that underlie this chromatin reorganization and their impact on embryogenesis in the nematode C. elegans. Full article
(This article belongs to the Special Issue DNA Organization in Model Organisms)
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Other

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25 pages, 3540 KiB  
Perspective
Transposon and Transgene Tribulations in Mosquitoes: A Perspective of piRNA Proportions
by Nelson C. Lau and Vanessa M. Macias
DNA 2024, 4(2), 104-128; https://doi.org/10.3390/dna4020006 - 30 Mar 2024
Viewed by 505
Abstract
Mosquitoes, like Drosophila, are dipterans, the order of “true flies” characterized by a single set of two wings. Drosophila are prime model organisms for biomedical research, while mosquito researchers struggle to establish robust molecular biology in these that are arguably the most [...] Read more.
Mosquitoes, like Drosophila, are dipterans, the order of “true flies” characterized by a single set of two wings. Drosophila are prime model organisms for biomedical research, while mosquito researchers struggle to establish robust molecular biology in these that are arguably the most dangerous vectors of human pathogens. Both insects utilize the RNA interference (RNAi) pathway to generate small RNAs to silence transposons and viruses, yet details are emerging that several RNAi features are unique to each insect family, such as how culicine mosquitoes have evolved extreme genomic feature differences connected to their unique RNAi features. A major technical difference in the molecular genetic studies of these insects is that generating stable transgenic animals are routine in Drosophila but still variable in stability in mosquitoes, despite genomic DNA-editing advances. By comparing and contrasting the differences in the RNAi pathways of Drosophila and mosquitoes, in this review we propose a hypothesis that transgene DNAs are possibly more intensely targeted by mosquito RNAi pathways and chromatin regulatory pathways than in Drosophila. We review the latest findings on mosquito RNAi pathways, which are still much less well understood than in Drosophila, and we speculate that deeper study into how mosquitoes modulate transposons and viruses with Piwi-interacting RNAs (piRNAs) will yield clues to improving transgene DNA expression stability in transgenic mosquitoes. Full article
(This article belongs to the Special Issue DNA Organization in Model Organisms)
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