Non Random Distribution of DMD Deletion Breakpoints and Implication of Double Strand Breaks Repair and Replication Error Repair Mechanisms

SummaryIonising irradiation acts primarily via induction of DNA damage, among which doublestrand breaks are the most important lesions. These lesions may lead to lethal chromosome aberrations, which are the main reason for cell inactivation. Double-strand breaks can be repaired by several different mechanisms. The regulation of these mechanisms appears be fairly different for normal and tumour cells. Among different cell lines capacity of doublestrand break repair varies by only few percents and is known to be determined mostly by genetic factors. Knowledge about doublestrand break repair mechanisms and their regulation is important for the optimal application of ionising irradiation in medicine.

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Live-cell chromosome dynamics in Arabidopsis thaliana reveals increased chromatin mobility in response to DNA damage

10.1101/2021.11.03.466744 ◽

2021 ◽

Author(s):

Anis Meschichi ◽

Adrien Sicard ◽

Frédéric Pontvianne ◽

Svenja Reeck ◽

Stefanie Rosa

Keyword(s):

Dna Damage ◽

Arabidopsis Thaliana ◽

Genome Instability ◽

High Mobility ◽

Double Strand Breaks ◽

Nuclear Space ◽

Strand Breaks ◽

Homologous Sequences ◽

Damage Response ◽

Repair Mechanisms

Double-strand breaks (DSBs) are a particularly deleterious type of DNA damage potentially leading to translocations and genome instability. Homologous recombination (HR) is a conservative repair pathway in which intact homologous sequences are used as a template for repair. How damaged DNA molecules search for homologous sequences in the crowded space of the cell nucleus is, however, still poorly understood, especially in plants. Here, we measured global chromosome and DSB site mobility, in Arabidopsis thaliana, by tracking the motion of specific loci using the lacO/LacI tagging system and two GFP-tagged HR regulators, RAD51 and RAD54. We observed an increase in chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. Importantly, this increase in mobility was lost on sog1-1 mutant, a central transcription factor of the DNA damage response (DDR), indicating that repair mechanisms actively regulate chromatin mobility upon DNA damage. Interestingly, we observed that DSB sites show remarkably high mobility levels at the early HR stage. Subsequently, a drastic decrease of DSB mobility is observed, which seems to be associated to the relocation of DSBs to the nucleus periphery. Altogether, our data suggest that changes in chromatin mobility are triggered in response to DNA damage, and that this may act as a mechanism to enhance the physical search within the nuclear space to locate a homologous template during homology-directed DNA repair.

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Non-random distribution of DNA double-strand breaks induced by particle irradiation

International Journal of Radiation Biology ◽

10.1080/095530096144680 ◽

1996 ◽

Vol 70 (5) ◽

pp. 493-503 ◽

Cited By ~ 145

Author(s):

M. LOBRICH, P. K. COOPER and B. RYDBER

Keyword(s):

Random Distribution ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Particle Irradiation

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TALEN-mediated genome editing: prospects and perspectives

Biochemical Journal ◽

10.1042/bj20140295 ◽

2014 ◽

Vol 462 (1) ◽

pp. 15-24 ◽

Cited By ~ 65

Author(s):

David A. Wright ◽

Ting Li ◽

Bing Yang ◽

Martin H. Spalding

Keyword(s):

Genome Editing ◽

Double Strand Breaks ◽

Zinc Finger Nucleases ◽

Transcription Activator ◽

Strand Breaks ◽

Natural Processes ◽

Current State ◽

A Genome ◽

Dna Dsbs ◽

Repair Mechanisms

Genome editing is the practice of making predetermined and precise changes to a genome by controlling the location of DNA DSBs (double-strand breaks) and manipulating the cell's repair mechanisms. This technology results from harnessing natural processes that have taken decades and multiple lines of inquiry to understand. Through many false starts and iterative technology advances, the goal of genome editing is just now falling under the control of human hands as a routine and broadly applicable method. The present review attempts to define the technique and capture the discovery process while following its evolution from meganucleases and zinc finger nucleases to the current state of the art: TALEN (transcription-activator-like effector nuclease) technology. We also discuss factors that influence success, technical challenges and future prospects of this quickly evolving area of study and application.

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DNA repair after oncological therapy (radiotherapy and chemotherapy)

Oxford Textbook of Oncology ◽

10.1093/med/9780199656103.003.0009_update_001 ◽

2016 ◽

pp. 82-85

Author(s):

Ekkehard Dikomey ◽

Kerstin Borgmann ◽

Malte Kriegs ◽

Wael Y. Mansour ◽

Cordula Petersen ◽

...

Keyword(s):

Dna Repair ◽

Genomic Stability ◽

Lethal Effect ◽

Tumour Cells ◽

Double Strand Breaks ◽

Radiation Response ◽

Dna Double Strand Breaks ◽

Dsb Repair ◽

Strand Breaks ◽

Repair Mechanisms

The lethal effect of ionizing irradiation on tumour cells is mostly determined by the repair of DNA double-strand breaks (DSBs). Cells are able to repair most of the DSBs, but 1% to 3 % are either non- or mis-repaired, which will then give rise to lethal chromosomal aberrations. Cells have evolved complex DSB repair mechanisms with a stringent hierarchy to guarantee the genomic stability. However, in tumour cells both mechanisms as well as hierarchy are often disturbed. This knowledge is important for an understanding of the radiation response of tumours, but—most of all—for the establishment of new and specific targets for therapy.

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Conservative Repair of a Chromosomal Double-Strand Break by Single-Strand DNA through Two Steps of Annealing

Molecular and Cellular Biology ◽

10.1128/mcb.00672-06 ◽

2006 ◽

Vol 26 (20) ◽

pp. 7645-7657 ◽

Cited By ~ 75

Author(s):

Francesca Storici ◽

Joyce R. Snipe ◽

Godwin K. Chan ◽

Dmitry A. Gordenin ◽

Michael A. Resnick

Keyword(s):

Normal Cell ◽

Strand Break ◽

Double Strand Breaks ◽

Single Strand ◽

Dsb Repair ◽

Strand Breaks ◽

Single Strand Annealing ◽

Repair Mechanisms ◽

Strand Invasion ◽

Strand Annealing

ABSTRACT The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null rad52 mutation. The repair did not involve Rad51-driven strand invasion, and moreover the suppression of strand invasion increased repair with oligonucleotides. A DSB was shown to activate targeting by oligonucleotides homologous to only one side of the break at large distances (at least 20 kb) from the break in a strand-biased manner, suggesting extensive 5′ to 3′ resection, followed by the restoration of resected DNA to the double-strand state. We conclude that long resected chromosomal DSB ends are repaired by a single-strand DNA oligonucleotide through two rounds of annealing. The repair by single-strand DNA can be conservative and may allow for accurate restoration of chromosomal DNAs with closely spaced DSBs.

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DNA Damage and Repair Mechanisms Triggered by Exposure to Bioflavonoids and Natural Compounds

10.5772/intechopen.95453 ◽

2021 ◽

Author(s):

Donna Goodenow ◽

Kiran Lalwani ◽

Christine Richardson

Keyword(s):

Dna Damage ◽

Cellular Response ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Environmental Agents ◽

Repair Mechanisms ◽

Alternative End Joining ◽

Differentiation Status

Eukaryotic cells use homologous recombination (HR), classical end-joining (C-NHEJ), and alternative end-joining (Alt-EJ) to repair DNA double-strand breaks (DSBs). Repair pathway choice is controlled by the activation and activity of pathways specific proteins in eukaryotes. Activity may be regulated by cell cycle stage, tissue type, and differentiation status. Bioflavonoids and other environmental agents such as pesticides have been shown to biochemically act as inhibitors of topoisomerase II (Top2). In cells, bioflavonoids directly lead to DNA double-strand breaks through both Top2-dependent and independent mechanisms, as well as induce DNA damage response (DDR) signaling, and promote alternative end-joining and chromosome alterations. This chapter will present differences in expression and activity of proteins in major DNA repair pathways, findings of Top2 inhibition by bioflavonoids and cellular response, discuss how these compounds trigger alternative end-joining, and conclude with implications for genome instability and human disease.

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FREQUENT GENE CONVERSION IN HUMAN EMBRYOS INDUCED BY DOUBLE STRAND BREAKS

10.1101/2020.06.19.162214 ◽

2020 ◽

Cited By ~ 6

Author(s):

Dan Liang ◽

Nuria Marti Gutierrez ◽

Tailai Chen ◽

Yeonmi Lee ◽

Sang-Wook Park ◽

...

Keyword(s):

Gene Conversion ◽

Safety Concern ◽

Cell Types ◽

Double Strand Breaks ◽

Human Embryos ◽

Gene Correction ◽

End Joining ◽

Strand Breaks ◽

Repair Mechanisms ◽

Non Homologous End Joining

AbstractApplications of genome editing ultimately depend on DNA repair triggered by targeted double-strand breaks (DSBs). However, repair mechanisms in human cells remain poorly understood and vary across different cell types. Here we report that DSBs selectively induced on a mutant allele in heterozygous human embryos are repaired by gene conversion using an intact wildtype homolog as a template in up to 40% of targeted embryos. We also show that targeting of homozygous loci facilitates an interplay of non-homologous end joining (NHEJ) and gene conversion and results in embryos which carry identical indel mutations on both loci. Additionally, conversion tracks may expand bidirectionally well beyond the target region leading to an extensive loss of heterozygosity (LOH). Our study demonstrates that gene conversion and NHEJ are two major DNA DSB repair mechanisms in preimplantation human embryos. While gene conversion could be applicable for gene correction, extensive LOH presents a serious safety concern.

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DNA repair after oncological therapy (radiotherapy and chemotherapy)

Oxford Textbook of Oncology ◽

10.1093/med/9780199656103.003.0009 ◽

2016 ◽

pp. 82-85

Author(s):

Ekkehard Dikomey ◽

Kerstin Borgmann ◽

Malte Kriegs ◽

Wael Y. Mansour ◽

Cordula Petersen ◽

...

Keyword(s):

Dna Repair ◽

Genomic Stability ◽

Lethal Effect ◽

Tumour Cells ◽

Double Strand Breaks ◽

Radiation Response ◽

Dna Double Strand Breaks ◽

Dsb Repair ◽

Strand Breaks ◽

Repair Mechanisms

The lethal effect of ionizing irradiation on tumour cells is mostly determined by the repair of DNA double-strand breaks (DSBs). Cells are able to repair most of the DSBs, but 1% to 3 % are either non- or mis-repaired, which will then give rise to lethal chromosomal aberrations. Cells have evolved complex DSB repair mechanisms with a stringent hierarchy to guarantee the genomic stability. However, in tumour cells both mechanisms as well as hierarchy are often disturbed. This knowledge is important for an understanding of the radiation response of tumours, but—most of all—for the establishment of new and specific targets for therapy.

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I-SceI Endonuclease, a New Tool for Studying DNA Double-Strand Break Repair Mechanisms in Drosophila

Genetics ◽

10.1093/genetics/152.3.1037 ◽

1999 ◽

Vol 152 (3) ◽

pp. 1037-1044 ◽

Cited By ~ 1

Author(s):

Yohanns Bellaiche ◽

Vladic Mogila ◽

Norbert Perrimon

Keyword(s):

Germ Line ◽

Marker Gene ◽

Strand Break ◽

Double Strand Breaks ◽

Drosophila Genome ◽

Strand Breaks ◽

Recombination System ◽

Dna Double Strand Break ◽

Repair Mechanisms ◽

Specific Position

Abstract As a step toward the development of a homologous recombination system in Drosophila, we have developed a methodology to target double-strand breaks (DSBs) to a specific position in the Drosophila genome. This method uses the mitochondrial endonuclease I-SceI that recognizes and cuts an 18-bp restriction site. We find that >6% of the progeny derived from males that carry a marker gene bordered by two I-SceI sites and that express I-SceI in their germ line lose the marker gene. Southern blot analysis and sequencing of the regions surrounding the I-SceI sites revealed that in the majority of the cases, the introduction of DSBs at the I-SceI sites resulted in the complete deletion of the marker gene; the other events were associated with partial deletion of the marker gene. We discuss a number of applications for this novel technique, in particular its use to study DSB repair mechanisms.

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