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Article: The Study of Cancer Susceptibility Genes.

Pavlov, Youri I

2021 Volume 13, Issue 9

Abstract: most complex, new direction for cancer medicine is to integrate our understanding of aberrant genes and pathways to explain the behavior of cancer as a whole, thereby renewing the cycle of knowledge, discovery and therapeutic intervention [ ... ]. ...

Abstract	"…most complex, new direction for cancer medicine is to integrate our understanding of aberrant genes and pathways to explain the behavior of cancer as a whole, thereby renewing the cycle of knowledge, discovery and therapeutic intervention [...].
Language	English
Publishing date	2021-05-08
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13092258
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Editorial: Emerging talents in genomic assay technology.

Reddi, Honey V / Pavlov, Youri I

Frontiers in genetics

2023 Volume 14, Page(s) 1259011

Language	English
Publishing date	2023-09-11
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1259011
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Polymorphism of

Zhuk, Anna S / Lada, Artem G / Pavlov, Youri I

International journal of molecular sciences

2023 Volume 24, Issue 9

Abstract: Baker's yeast, ...

Abstract	Baker's yeast,
MeSH term(s)	Humans ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Polymorphism, Genetic ; Saccharomyces cerevisiae Proteins/metabolism ; Genomic Instability ; DNA/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2023-04-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24097795
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CRISPR/Cas9 as a Mutagenic Factor.

Shumega, Andrey R / Pavlov, Youri I / Chirinskaite, Angelina V / Rubel, Aleksandr A / Inge-Vechtomov, Sergey G / Stepchenkova, Elena I

International journal of molecular sciences

2024 Volume 25, Issue 2

Abstract: The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target ... ...

Abstract	The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target sites and, unfortunately, at off-target genome sites. DNA repair systems differing in accuracy participate in establishing desired genetic changes but also introduce unwanted mutations, that may lead to hereditary, oncological, and other diseases. New approaches to alleviate the risks associated with genome editing include attenuating the off-target activity of editing complex through the use of modified forms of Cas9 nuclease and single guide RNA (sgRNA), improving delivery methods for sgRNA/Cas9 complex, and directing DNA lesions caused by the sgRNA/Cas9 to non-mutagenic repair pathways. Here, we have described CRISPR/Cas9 as a new powerful mutagenic factor, discussed its mutagenic properties, and reviewed factors influencing the mutagenic activity of CRISPR/Cas9.
MeSH term(s)	Mutagens ; CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems ; Mutagenesis/genetics ; Mutation
Chemical Substances	Mutagens ; RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2024-01-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25020823
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Article ; Online: DNA Polymerase ζ without the C-Terminus of Catalytic Subunit Rev3 Retains Characteristic Activity, but Alters Mutation Specificity of Ultraviolet Radiation in Yeast.

Siebler, Hollie M / Cui, Jian / Hill, Sarah E / Pavlov, Youri I

Genes

2022 Volume 13, Issue 9

Abstract: DNA polymerase ζ (pol ζ) plays a central role in replicating damaged genomic DNA. When DNA synthesis stalls at a lesion, it participates in translesion DNA synthesis (TLS), which helps replication proceed. TLS prevents cell death at the expense of new ... ...

Abstract	DNA polymerase ζ (pol ζ) plays a central role in replicating damaged genomic DNA. When DNA synthesis stalls at a lesion, it participates in translesion DNA synthesis (TLS), which helps replication proceed. TLS prevents cell death at the expense of new mutations. The current model indicates that pol ζ-dependent TLS events are mediated by Pol31/Pol32 pol ζ subunits, which are shared with replicative polymerase pol δ. Surprisingly, we found that the mutant
MeSH term(s)	Catalytic Domain/genetics ; DNA/metabolism ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Mutation ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Ultraviolet Rays/adverse effects
Chemical Substances	DNA (9007-49-2) ; DNA polymerase zeta (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2022-09-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13091576
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Correction: Pavlov, Y.I., et al. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years After: Connection to Cancer.

Pavlov, Youri I / Zhuk, Anna S / Stepchenkova, Elena I

Cancers

2021 Volume 13, Issue 5

Abstract: The authors wish to make the following corrections to this paper [ ... ]. ...

Abstract	The authors wish to make the following corrections to this paper [...].
Language	English
Publishing date	2021-02-26
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13050969
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Article ; Online: Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2.

Rogozin, Igor B / Saura, Andreu / Poliakov, Eugenia / Bykova, Anastassia / Roche-Lima, Abiel / Pavlov, Youri I / Yurchenko, Vyacheslav

International journal of molecular sciences

2024 Volume 25, Issue 7

Abstract: SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical ... ...

Abstract	SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
MeSH term(s)	Humans ; COVID-19/genetics ; SARS-CoV-2/genetics ; Mutagenesis ; Mutation ; Nucleotides
Chemical Substances	Nucleotides
Language	English
Publishing date	2024-03-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25073696
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Article: DNA Polymerase ζ without the C-Terminus of Catalytic Subunit Rev3 Retains Characteristic Activity, but Alters Mutation Specificity of Ultraviolet Radiation in Yeast

Siebler, Hollie M. / Cui, Jian / Hill, Sarah E. / Pavlov, Youri I.

Genes. 2022 Sept. 02, v. 13, no. 9

2022

Abstract	DNA polymerase ζ (pol ζ) plays a central role in replicating damaged genomic DNA. When DNA synthesis stalls at a lesion, it participates in translesion DNA synthesis (TLS), which helps replication proceed. TLS prevents cell death at the expense of new mutations. The current model indicates that pol ζ-dependent TLS events are mediated by Pol31/Pol32 pol ζ subunits, which are shared with replicative polymerase pol δ. Surprisingly, we found that the mutant rev3-ΔC in yeast, which lacks the C-terminal domain (CTD) of the catalytic subunit of pol ζ and, thus, the platform for interaction with Pol31/Pol32, retains most pol ζ functions. To understand the underlying mechanisms, we studied TLS in normal templates or templates with abasic sites in vitro in primer extension reactions with purified four-subunit pol ζ versus pol ζ with Rev3-ΔC. We also examined the specificity of ultraviolet radiation (UVR)-induced mutagenesis in the rev3-ΔC strains. We found that the absence of Rev3 CTD reduces activity levels, but does not alter the basic biochemical properties of pol ζ, and alters the mutation spectrum only at high doses of UVR, alluding to the existence of mechanisms of recruitment of pol ζ to UVR-damaged sites independent of the interaction of Pol31/Pol32 with the CTD of Rev3.
Keywords	DNA ; DNA replication ; DNA-directed DNA polymerase ; amino acid sequences ; cell death ; models ; mutagenesis ; mutants ; protein subunits ; ultraviolet radiation ; yeasts
Language	English
Dates of publication	2022-0902
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13091576
Database	NAL-Catalogue (AGRICOLA)

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Article: DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer.

Pavlov, Youri I / Zhuk, Anna S / Stepchenkova, Elena I

Cancers

2020 Volume 12, Issue 12

Abstract: Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of ... ...

Abstract	Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named "division of labor," remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants' effects on cancer.
Language	English
Publishing date	2020-11-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers12123489
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Article ; Online: Partners in crime: Tbf1 and Vid22 promote expansions of long human telomeric repeats at an interstitial chromosome position in yeast.

Radchenko, Elina A / Aksenova, Anna Y / Volkov, Kirill V / Shishkin, Alexander A / Pavlov, Youri I / Mirkin, Sergei M

PNAS nexus

2022 Volume 1, Issue 3, Page(s) pgac080

Abstract: In humans, telomeric repeats (TTAGGG) ...

Abstract	In humans, telomeric repeats (TTAGGG)
Language	English
Publishing date	2022-06-08
Publishing country	England
Document type	Journal Article
ISSN	2752-6542
ISSN (online)	2752-6542
DOI	10.1093/pnasnexus/pgac080
Database	MEDical Literature Analysis and Retrieval System OnLINE

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