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Mechanisms of DNA Repair in the Context of Transcription, Replication...
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Mechanisms of DNA Repair in the Context of Transcription, Replication and Recombination

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biophysics".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 19201

Special Issue Editors

Dr. Harshad Ghodke

E-Mail Website
Guest Editor
School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine & Health, University of Wollongong, NSW 2522, Australia
Interests: DNA repair; single-molecule fluorescence imaging; live-cell imaging; single-molecule biophysics; protein-DNA interactions
Dr. Elise Fouquerel

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Room 830, Philadelphia, PA 19107, USA
Interests: Poly(ADP-ribosyl)ation; PARP; DNA repair; base excision repair; oxidative stress; telomeres and telomerase; genome integrity; aging; cancer

Special Issue Information

Maintaining genomic integrity in the background of on-going DNA metabolism is a challenge faced by all living organisms. Often, DNA repair factors must interface with transcription, replication and recombination machineries to efficiently recognize DNA damage and repair it rapidly to enable DNA metabolism to continue. With varying extents of conservation of transcription, replication and recombination machineries across the kingdoms of life, it is no surprise that DNA repair factors are often poorly conserved across species. This Special Issue aims to review advances in our knowledge of molecular mechanisms of DNA repair obtained using structural, biochemical and biophysical approaches from diverse model organisms. To that end, we invite original research articles and reviews that cover various aspects of DNA repair in the context of replication, transcription and recombination, including DNA damage detection and signaling, the role of post-translational modifications, co-ordination of handoffs, pathway choice gathered from in vitro and in vivo structural and biophysical techniques. We also encourage the submission of articles that describe development of novel methods for studying DNA repair.

Dr. Harshad Ghodke
Dr. Elise Fouquerel
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. Biology 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

  • DNA repair 
  • DNA replication 
  • Transcription 
  • Recombination 
  • Biophysics 
  • Microscopy 
  • Live-cell imaging 
  • Structural biology 
  • Molecular mechanisms 
  • Enzymology

Published Papers (5 papers)

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Research

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15 pages, 2538 KiB  
Article
Associations between DNA Damage and PD-L1 Expression in Ovarian Cancer, a Potential Biomarker for Clinical Response
by Elise K. Mann, Kevin J. Lee, Dongquan Chen, Luciana Madeira da Silva, Valeria L. Dal Zotto, Jennifer Scalici and Natalie R. Gassman
Biology 2021, 10(5), 385; https://doi.org/10.3390/biology10050385 - 29 Apr 2021
Cited by 5 | Viewed by 2707
Abstract
Programmed death ligand-1 (PD-L1) inhibitors are currently under investigation as a potential treatment option for ovarian cancer. Although this therapy has shown promise, its efficacy is highly variable among patients. Evidence suggests that genomic instability influences the expression of PD-L1, but little is [...] Read more.
Programmed death ligand-1 (PD-L1) inhibitors are currently under investigation as a potential treatment option for ovarian cancer. Although this therapy has shown promise, its efficacy is highly variable among patients. Evidence suggests that genomic instability influences the expression of PD-L1, but little is known about this relationship in ovarian cancer. To examine the relationship between PD-L1 expression and genomic instability, we measured DNA damage using Repair Assisted Damage Detection (RADD). We then correlated the presence of persistent DNA damage in the ovarian tumor with protein expression of PD-L1 using immunohistochemistry. Ovarian tumors showed a high prevalence of oxidative DNA damage. As the level of oxidative DNA damage increased, we saw a significant correlation with PD-L1 expression. The highest correlation between DNA damage and PD-L1 expression was observed for mucinous ovarian tumors (r = 0.82), but a strong correlation was also observed for high grade serous and endometrioid tumors (r = 0.67 and 0.69, respectively). These findings link genomic instability to PD-L1 protein expression in ovarian cancer and suggest that persistent DNA damage can be used as a potential biomarker for patient selection for immunotherapy treatment. Full article
(This article belongs to the Special Issue Mechanisms of DNA Repair in the Context of Transcription, Replication and Recombination)
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Review

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40 pages, 5406 KiB  
Review
Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair
by Marlo K. Thompson, Robert W. Sobol and Aishwarya Prakash
Biology 2021, 10(6), 530; https://doi.org/10.3390/biology10060530 - 14 Jun 2021
Cited by 5 | Viewed by 5557
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant [...] Read more.
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples. Full article
(This article belongs to the Special Issue Mechanisms of DNA Repair in the Context of Transcription, Replication and Recombination)
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15 pages, 1836 KiB  
Review
Towards a Structural Mechanism for Sister Chromatid Cohesion Establishment at the Eukaryotic Replication Fork
by Sarah S. Henrikus and Alessandro Costa
Biology 2021, 10(6), 466; https://doi.org/10.3390/biology10060466 - 26 May 2021
Cited by 1 | Viewed by 3446
Abstract
Cohesion between replicated chromosomes is essential for chromatin dynamics and equal segregation of duplicated genetic material. In the G1 phase, the ring-shaped cohesin complex is loaded onto duplex DNA, enriching at replication start sites, or “origins”. During the same phase of the cell [...] Read more.
Cohesion between replicated chromosomes is essential for chromatin dynamics and equal segregation of duplicated genetic material. In the G1 phase, the ring-shaped cohesin complex is loaded onto duplex DNA, enriching at replication start sites, or “origins”. During the same phase of the cell cycle, and also at the origin sites, two MCM helicases are loaded as symmetric double hexamers around duplex DNA. During the S phase, and through the action of replication factors, cohesin switches from encircling one parental duplex DNA to topologically enclosing the two duplicated DNA filaments, which are known as sister chromatids. Despite its vital importance, the structural mechanism leading to sister chromatid cohesion establishment at the replication fork is mostly elusive. Here we review the current understanding of the molecular interactions between the replication machinery and cohesin, which support sister chromatid cohesion establishment and cohesin function. In particular, we discuss how cryo-EM is shedding light on the mechanisms of DNA replication and cohesin loading processes. We further expound how frontier cryo-EM approaches, combined with biochemistry and single-molecule fluorescence assays, can lead to understanding the molecular basis of sister chromatid cohesion establishment at the replication fork. Full article
(This article belongs to the Special Issue Mechanisms of DNA Repair in the Context of Transcription, Replication and Recombination)
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18 pages, 1770 KiB  
Review
Elucidating Recombination Mediator Function Using Biophysical Tools
by Camille Henry and Sarah S. Henrikus
Biology 2021, 10(4), 288; https://doi.org/10.3390/biology10040288 - 1 Apr 2021
Cited by 4 | Viewed by 2760
Abstract
The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products [...] Read more.
The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context. Full article
(This article belongs to the Special Issue Mechanisms of DNA Repair in the Context of Transcription, Replication and Recombination)
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Other

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27 pages, 3675 KiB  
Protocol
Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules
by Max S. Fairlamb, Amy M. Whitaker, Fletcher E. Bain, Maria Spies and Bret D. Freudenthal
Biology 2021, 10(7), 571; https://doi.org/10.3390/biology10070571 - 23 Jun 2021
Cited by 5 | Viewed by 3886
Abstract
Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. [...] Read more.
Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope which can be utilized for the study of macromolecular complexes, including the multi-component protein–DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology. Full article
(This article belongs to the Special Issue Mechanisms of DNA Repair in the Context of Transcription, Replication and Recombination)
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