Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Molecular Research of DNA Replication and Genome Stability

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

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 April 2021) | Viewed by 25069

Share This Special Issue

Special Issue Editor

Dr. Francesca M. Pisani

E-Mail Website
Guest Editor

Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, 80131 Napoli, Italy
Interests: DNA replication; Genome stability; Sister chromatid cohesion; DNA enzymes

Special Issue Information

Dear Colleagues,

The duplication of chromosomal DNA is executed in the cell by a complex multi-protein machine named the “replisome”. It includes at least three different DNA polymerases, one DNA primase (a specialised RNA polymerase) and one DNA helicase. These enzymes must work together at the replication fork in a coordinated way to ensure complete, fast and accurate replication of the genome. The accuracy of this process is critical for short-term cell survival. On the other hand, the rare mutations that occur are important for the long-term survival of species, because they provide the genetic variations upon which selection pressures act during biological evolution. Since the seminal discovery of the first enzyme able to catalyze the template-directed synthesis of DNA (DNA polymerase I of Escherichia coli) by Arthur Kornberg in 1955, enzymes working at the replication forks (along with their auxiliary subunits and regulators) have been the subject of intensive investigations. Nonetheless, a lot has yet to be learned about the molecular mechanisms underlying the DNA replication process: the coordination of genome duplication with other critical chromosomal transactions (i.e., epigenetic mark heritage, sister chromatid cohesion, chromosome segregation, gene transcription) is largely unexplored. The availability of novel tools to manipulate genes of interest in mammalian cells and recent improvement of the bio-imaging technologies (including the implementation of user-friendly optical tweezer-based instruments for single-molecule biophysical studies) are leading to a more comprehensive understanding of the molecular and cellular functions of the enzymes/proteins involved in the genome stability maintenance pathways. This Special Issue of the International Journal of Molecular Sciences will collect contributions along these lines of investigation.

Dr. Francesca M. Pisani
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 replication
DNA repair
DNA recombination
Genome stability
Sister chromatid cohesion
DNA enzymes
Single-molecule biophysical studies

Published Papers (6 papers)

Download All Papers

Research

Jump to: Review

16 pages, 3619 KiB

Open AccessArticle

High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures

by Maria Dede, Silvia Napolitano, Anna Melati, Valentina Pirota, Giovanni Maga and Emmanuele Crespan

Int. J. Mol. Sci. 2021, 22(10), 5201; https://doi.org/10.3390/ijms22105201 - 14 May 2021

Cited by 1 | Viewed by 2791

Abstract

Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2′-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA replication causing replicative fork stalling and collapse. Ribonucleotide removal is initiated by Ribonuclease H2 (RNase H2), the key player in Ribonucleotide Excision Repair (RER). Its absence leads to embryonic lethality in mice, while mutations decreasing its activity cause Aicardi–Goutières syndrome. DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form. Ribonucleotides pairing to lesioned nucleotides, or incorporated within non-B DNA structures could avoid RNase H2 recognition, potentially contributing to genome instability. In this work, we investigate the ability of RNase H2 to process misincorporated ribonucleotides in a panel of DNA substrates showing different geometrical features. RNase H2 proved to be a flexible enzyme, recognizing as a substrate the majority of the constructs we generated. However, some geometrical features and non-canonical DNA structures severely impaired its activity, suggesting a relevant role of misincorporated ribonucleotides in the physiological instability of specific DNA sequences. Full article

(This article belongs to the Special Issue Molecular Research of DNA Replication and Genome Stability)

► Show Figures

Graphical abstract

17 pages, 3531 KiB

Open AccessArticle

Clearing of Foreign Episomal DNA from Human Cells by CRISPRa-Mediated Activation of Cytidine Deaminases

by Sergey Brezgin, Anastasiya Kostyusheva, Natalia Ponomareva, Viktoriia Volia, Irina Goptar, Anastasiya Nikiforova, Igor Shilovskiy, Valery Smirnov, Dmitry Kostyushev and Vladimir Chulanov

Int. J. Mol. Sci. 2020, 21(18), 6865; https://doi.org/10.3390/ijms21186865 - 18 Sep 2020

Cited by 6 | Viewed by 2583

Abstract

Restriction of foreign DNA is a fundamental defense mechanism required for maintaining genomic stability and proper function of mammalian cells. APOBEC cytidine deaminases are crucial effector molecules involved in clearing pathogenic DNA of viruses and other microorganisms and improperly localized self-DNA (DNA leakages). Mastering the expression of APOBEC provides the crucial means both for developing novel therapeutic approaches for combating infectious and non-infectious diseases and for numerous research purposes. In this study, we report successful application of a CRISPRa approach to effectively and specifically overexpress APOBEC3A and APOBEC3B deaminases and describe their effects on episomal and integrated foreign DNA. This method increased target gene transcription by >6–50-fold in HEK293T cells. Furthermore, CRISPRa-mediated activation of APOBEC3A/APOBEC3B suppressed episomal but not integrated foreign DNA. Episomal GC-rich DNA was rapidly destabilized and destroyed by CRISPRa-induced APOBEC3A/APOBEC3B, while the remaining DNA templates harbored frequent deaminated nucleotides. To conclude, the CRISPRa approach could be readily utilized for manipulating innate immunity and investigating the effects of the key effector molecules on foreign nucleic acids. Full article

(This article belongs to the Special Issue Molecular Research of DNA Replication and Genome Stability)

► Show Figures

Figure 1

16 pages, 1348 KiB

Open AccessArticle

Shoot Tip Cryopreservation of Lamprocapnos spectabilis (L.) Fukuhara Using Different Approaches and Evaluation of Stability on the Molecular, Biochemical, and Plant Architecture Levels

by Dariusz Kulus

Int. J. Mol. Sci. 2020, 21(11), 3901; https://doi.org/10.3390/ijms21113901 - 30 May 2020

Cited by 16 | Viewed by 2341

Abstract

The aim of this study is to optimize and evaluate the effectiveness of vitrification, droplet-vitrification, and encapsulation-vitrification techniques in the cryopreservation of Lamprocapnos spectabilis (L.) Fukuhara ‘Gold Heart’, a popular medicinal and ornamental plant species. In vitro-derived shoot tips were used in the experiments. All three techniques were based on explant dehydration with plant vitrification solution 3 (PVS3; 50% glycerol and 50% sucrose) for 0, 30, 60, 90, 120, 150, or 180 min. The recovered microshoots were subjected to morphometric, biochemical, and molecular analyses (RAPD, ISSR, SCoT). The highest recovery level was reported with the encapsulation-vitrification protocol based on 150 min dehydration (73.1%), while the vitrification technique was the least effective (maximum 25.8% recovery). Explants cryopreserved with the encapsulation-vitrification technique produced the highest mean number of shoots (4.9); moreover, this technique was optimal in terms of rooting efficiency. The highest fresh weight of shoots, on the other hand, was found with the vitrification protocol based on a 30-min PVS3 treatment. The concentrations of chlorophyll a and b were lower in all cryopreservation-derived plants, compared to the untreated control. On the other hand, short dehydration and cryopreservation of non-encapsulated explants stimulated the synthesis of anthocyanins. A small genetic variation in 5% of all samples analyzed was detected by RAPD and ISSR marker systems. Only plants recovered from the encapsulation-vitrification protocol had no DNA sequence alternations. Full article

(This article belongs to the Special Issue Molecular Research of DNA Replication and Genome Stability)

► Show Figures

Figure 1

Review

Jump to: Research

15 pages, 2761 KiB

Open AccessReview

Functional Coupling between DNA Replication and Sister Chromatid Cohesion Establishment

by Ana Boavida, Diana Santos, Mohammad Mahtab and Francesca M. Pisani

Int. J. Mol. Sci. 2021, 22(6), 2810; https://doi.org/10.3390/ijms22062810 - 10 Mar 2021

Cited by 2 | Viewed by 3375

Abstract

Several lines of evidence suggest the existence in the eukaryotic cells of a tight, yet largely unexplored, connection between DNA replication and sister chromatid cohesion. Tethering of newly duplicated chromatids is mediated by cohesin, an evolutionarily conserved hetero-tetrameric protein complex that has a ring-like structure and is believed to encircle DNA. Cohesin is loaded onto chromatin in telophase/G1 and converted into a cohesive state during the subsequent S phase, a process known as cohesion establishment. Many studies have revealed that down-regulation of a number of DNA replication factors gives rise to chromosomal cohesion defects, suggesting that they play critical roles in cohesion establishment. Conversely, loss of cohesin subunits (and/or regulators) has been found to alter DNA replication fork dynamics. A critical step of the cohesion establishment process consists in cohesin acetylation, a modification accomplished by dedicated acetyltransferases that operate at the replication forks. Defects in cohesion establishment give rise to chromosome mis-segregation and aneuploidy, phenotypes frequently observed in pre-cancerous and cancerous cells. Herein, we will review our present knowledge of the molecular mechanisms underlying the functional link between DNA replication and cohesion establishment, a phenomenon that is unique to the eukaryotic organisms. Full article

(This article belongs to the Special Issue Molecular Research of DNA Replication and Genome Stability)

► Show Figures

Figure 1

23 pages, 1245 KiB

Open AccessReview

One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA

by Giulia Maria Nava, Lavinia Grasso, Sarah Sertic, Achille Pellicioli, Marco Muzi Falconi and Federico Lazzaro

Int. J. Mol. Sci. 2020, 21(5), 1706; https://doi.org/10.3390/ijms21051706 - 2 Mar 2020

Cited by 16 | Viewed by 6719

Abstract

In the last decade, it has become evident that RNA is frequently found in DNA. It is now well established that single embedded ribonucleoside monophosphates (rNMPs) are primarily introduced by DNA polymerases and that longer stretches of RNA can anneal to DNA, generating RNA:DNA hybrids. Among them, the most studied are R-loops, peculiar three-stranded nucleic acid structures formed upon the re-hybridization of a transcript to its template DNA. In addition, polyribonucleotide chains are synthesized to allow DNA replication priming, double-strand breaks repair, and may as well result from the direct incorporation of consecutive rNMPs by DNA polymerases. The bright side of RNA into DNA is that it contributes to regulating different physiological functions. The dark side, however, is that persistent RNA compromises genome integrity and genome stability. For these reasons, the characterization of all these structures has been under growing investigation. In this review, we discussed the origin of single and multiple ribonucleotides in the genome and in the DNA of organelles, focusing on situations where the aberrant processing of RNA:DNA hybrids may result in multiple rNMPs embedded in DNA. We concluded by providing an overview of the currently available strategies to study the presence of single and multiple ribonucleotides in DNA in vivo. Full article

(This article belongs to the Special Issue Molecular Research of DNA Replication and Genome Stability)

► Show Figures

Figure 1

27 pages, 1621 KiB

Open AccessReview

From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork

by Antonio Maffia, Cecilia Ranise and Simone Sabbioneda

Int. J. Mol. Sci. 2020, 21(4), 1506; https://doi.org/10.3390/ijms21041506 - 22 Feb 2020

Cited by 22 | Viewed by 6488

Abstract

Replicating the entire genome is one of the most complex tasks for all organisms. Research carried out in the last few years has provided us with a clearer picture on how cells preserve genomic information from the numerous insults that may endanger its stability. Different DNA repair pathways, coping with exogenous or endogenous threat, have been dissected at the molecular level. More recently, there has been an increasing interest towards intrinsic obstacles to genome replication, paving the way to a novel view on genomic stability. Indeed, in some cases, the movement of the replication fork can be hindered by the presence of stable DNA: RNA hybrids (R-loops), the folding of G-rich sequences into G-quadruplex structures (G4s) or repetitive elements present at Common Fragile Sites (CFS). Although differing in their nature and in the way they affect the replication fork, all of these obstacles are a source of replication stress. Replication stress is one of the main hallmarks of cancer and its prevention is becoming increasingly important as a target for future chemotherapeutics. Here we will try to summarize how these three obstacles are generated and how the cells handle replication stress upon their encounter. Finally, we will consider their role in cancer and their exploitation in current chemotherapeutic approaches. Full article

(This article belongs to the Special Issue Molecular Research of DNA Replication and Genome Stability)

► Show Figures