DNA Double-Strand Breaks: A Double-Edged Sword for Trypanosomatids

For nearly all eukaryotic cells, stochastic DNA double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions. DSB processing and repair can cause sequence deletions, loss of heterozygosity, and chromosome rearrangements resulting in cell death or carcinogenesis. However, trypanosomatids (single-celled eukaryotes parasites) do not seem to follow this premise strictly. Several studies have shown that trypanosomatids depend on DSBs to perform several events of paramount importance during their life cycle. For Trypanosoma brucei, DSBs formation is associated with host immune evasion via antigenic variation. In Trypanosoma cruzi, DSBs play a crucial role in the genetic exchange, a mechanism that is still little explored but appear to be of fundamental importance for generating variability. In Leishmania spp., DSBs are necessary to generate genomic changes by gene copy number variation (CNVs), events that are essential for these organisms to overcome inhospitable conditions. As DSB repair in trypanosomatids is primarily conducted via homologous recombination (HR), most of the events associated with DSBs are HR-dependent. This review will discuss the latest findings on how trypanosomatids balance the benefits and inexorable challenges caused by DSBs.

Transcription-induced formation of extrachromosomal DNA during yeast ageing

10.1101/744896 ◽

2019 ◽

Author(s):

Ryan Hull ◽

Michelle King ◽

Grazia Pizza ◽

Felix Krueger ◽

Xabier Vergara ◽

...

Keyword(s):

Copy Number ◽

De Novo ◽

Gene Copy Number ◽

Phenotypic Selection ◽

Copper Resistance ◽

Gene Copy ◽

Dna Double Strand Breaks ◽

Protein Coding ◽

Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation, and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper resistance gene CUP1. Transcription of CUP1 causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2 / Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant we find that CUP1 eccDNA does not replicate efficiently, and high copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment.

Faculty Opinions recommendation of Diet and the evolution of human amylase gene copy number variation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1092307.546722 ◽

2007 ◽

Author(s):

Magnus Ingelman-Sundberg

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Amylase Gene ◽

What a finding of gene copy number variation can add to the diagnosis of developmental neuropsychiatric disorders

Current Opinion in Genetics & Development ◽

10.1016/j.gde.2020.12.017 ◽

2021 ◽

Vol 68 ◽

pp. 18-25

Author(s):

Jacob Vorstman ◽

Stephen W Scherer

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Gene Copy Number ◽

Neuropsychiatric Disorders ◽

Gene Copy ◽

Focused Ion Microbeam Irradiation Induces Clustering of DNA Double-Strand Breaks in Heterochromatin Visualized by Nanoscale-Resolution Electron Microscopy

International Journal of Molecular Sciences ◽

10.3390/ijms22147638 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7638

Author(s):

Yvonne Lorat ◽

Judith Reindl ◽

Anna Isermann ◽

Christian Rübe ◽

Anna A. Friedl ◽

...

Keyword(s):

Electron Microscopy ◽

Dna Damage ◽

Spatial Clustering ◽

Dna Lesions ◽

Double Strand Breaks ◽

Stimulated Emission ◽

Nuclear Chromatin ◽

Carbon Ions ◽

Dna Double Strand Breaks ◽

Strand Breaks

Background: Charged-particle radiotherapy is an emerging treatment modality for radioresistant tumors. The enhanced effectiveness of high-energy particles (such as heavy ions) has been related to the spatial clustering of DNA lesions due to highly localized energy deposition. Here, DNA damage patterns induced by single and multiple carbon ions were analyzed in the nuclear chromatin environment by different high-resolution microscopy approaches. Material and Methods: Using the heavy-ion microbeam SNAKE, fibroblast monolayers were irradiated with defined numbers of carbon ions (1/10/100 ions per pulse, ipp) focused to micrometer-sized stripes or spots. Radiation-induced lesions were visualized as DNA damage foci (γH2AX, 53BP1) by conventional fluorescence and stimulated emission depletion (STED) microscopy. At micro- and nanoscale level, DNA double-strand breaks (DSBs) were visualized within their chromatin context by labeling the Ku heterodimer. Single and clustered pKu70-labeled DSBs were quantified in euchromatic and heterochromatic regions at 0.1 h, 5 h and 24 h post-IR by transmission electron microscopy (TEM). Results: Increasing numbers of carbon ions per beam spot enhanced spatial clustering of DNA lesions and increased damage complexity with two or more DSBs in close proximity. This effect was detectable in euchromatin, but was much more pronounced in heterochromatin. Analyzing the dynamics of damage processing, our findings indicate that euchromatic DSBs were processed efficiently and repaired in a timely manner. In heterochromatin, by contrast, the number of clustered DSBs continuously increased further over the first hours following IR exposure, indicating the challenging task for the cell to process highly clustered DSBs appropriately. Conclusion: Increasing numbers of carbon ions applied to sub-nuclear chromatin regions enhanced the spatial clustering of DSBs and increased damage complexity, this being more pronounced in heterochromatic regions. Inefficient processing of clustered DSBs may explain the enhanced therapeutic efficacy of particle-based radiotherapy in cancer treatment.

Induction of direct repeat recombination by psoralen–DNA adducts in Saccharomyces cerevisiae: Defects in DNA repair increase gene copy number variation

DNA Repair ◽

10.1016/j.dnarep.2014.05.011 ◽

2014 ◽

Vol 21 ◽

pp. 87-96 ◽

Cited By ~ 2

Author(s):

Wilma A. Saffran ◽

Anam Ahmed ◽

Olga Binyaminov ◽

Cynthia Gonzalez ◽

Amita Gupta ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Repair ◽

Copy Number Variation ◽

Dna Adducts ◽

Copy Number ◽

Gene Copy Number ◽

Direct Repeat ◽

Gene Copy ◽

Genetic variability of CYP2D6, CYP3A4 and CYP3A5 among the Egyptian population

Pharmacogenomics ◽

10.2217/pgs-2020-0140 ◽

2021 ◽

Author(s):

Thuraya M Mutawi ◽

Mohamed M Zedan ◽

Raida S Yahya ◽

Mahmoud M Zakria ◽

Mamdouh R El-Sawi ◽

...

Keyword(s):

Genetic Variability ◽

Copy Number Variation ◽

Copy Number ◽

Middle Eastern ◽

Gene Copy Number ◽

Gene Copy ◽

Allelic Variants ◽

Number Variation ◽

Study Participants

Aim: This study investigated major allelic variants of CYP2D6, CYP3A4 and CYP3A5 in Egyptians, an Arabic population for which there is little information regarding these important pharmacogenes. Patients & methods: CYP2D6*2, *4, *5, *10, *41 and gene copy number variation, as well as CYP3A4*22 and CYP3A5*3 were determined with commercially available TaqMan assays in 145 healthy study participants. Results: The CYP2D6 alleles identified suggest that the prevalence of poor metabolizers is low as none were found among the 145 subjects investigated. The frequency for CYP3A5 nonexpressers was 74.5% and the CYP3A4*22 allele frequency was low at 2.0%. Conclusion: These preliminary findings indicate that pharmacogene variation in Egyptians is different from those of other Middle Eastern/Arabic populations and warrants further investigation.