scholarly journals Genome-Wide Adductomics Analysis Reveals Heterogeneity in the Induction and Loss of Cyclobutane Thymine Dimers across Both the Nuclear and Mitochondrial Genomes

2019 ◽  
Vol 20 (20) ◽  
pp. 5112 ◽  
Author(s):  
Alaa S. Alhegaili ◽  
Yunhee Ji ◽  
Nicolas Sylvius ◽  
Matthew J. Blades ◽  
Mahsa Karbaschi ◽  
...  
Keyword(s):  
Dna Damage ◽  
Nuclear Dna ◽  
Mitochondrial Genomes ◽  
Differential Distribution ◽  
Dna Damage And Repair ◽  
Specific Level ◽  
Genome Wide ◽  
A Genome ◽  
High Resolution Map ◽  
Cellular Dna

The distribution of DNA damage and repair is considered to occur heterogeneously across the genome. However, commonly available techniques, such as the alkaline comet assay or HPLC-MS/MS, measure global genome levels of DNA damage, and do not reflect potentially significant events occurring at the gene/sequence-specific level, in the nuclear or mitochondrial genomes. We developed a method, which comprises a combination of Damaged DNA Immunoprecipitation and next generation sequencing (DDIP-seq), to assess the induction and repair of DNA damage induced by 0.1 J/cm2 solar-simulated radiation at the sequence-specific level, across both the entire nuclear and mitochondrial genomes. DDIP-seq generated a genome-wide, high-resolution map of cyclobutane thymine dimer (T<>T) location and intensity. In addition to being a straightforward approach, our results demonstrated a clear differential distribution of T<>T induction and loss, across both the nuclear and mitochondrial genomes. For nuclear DNA, this differential distribution existed at both the sequence and chromosome level. Levels of T<>T were much higher in the mitochondrial DNA, compared to nuclear DNA, and decreased with time, confirmed by qPCR, despite no reported mechanisms for their repair in this organelle. These data indicate the existence of regions of sensitivity and resistance to damage formation, together with regions that are fully repaired, and those for which > 90% of damage remains, after 24 h. This approach offers a simple, yet more detailed approach to studying cellular DNA damage and repair, which will aid our understanding of the link between DNA damage and disease.

scholarly journals Genome wide mapping of DNA lesions by Repair Assisted Damage Detection sequencing – RADD-Seq

2021 ◽  
Author(s):  
Noa Gilat ◽  
Dena Fridman ◽  
Hila Sharim ◽  
Sapir Margalit ◽  
Natalie R. Gassman ◽  
...  
Keyword(s):  
Dna Damage ◽  
Damage Detection ◽  
Oxidative Dna Damage ◽  
Dna Lesions ◽  
Open Chromatin ◽  
Dna Damage And Repair ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Before And After

AbstractMapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, like cancer, and assists in monitoring their progression and prognosis. However, genome-wide maps of DNA damage distribution are challenging to produce. Here we describe the localization of DNA damage and repair loci by Repair Assisted Damage Detection sequencing – RADD-Seq. Based on the enrichment of damage lesions coupled with a pull-down assay and followed by next generation sequencing, this method is easy to perform and can produce compelling results with minimal coverage. RADD-seq enables the localization of both DNA damage and repair sites for a wide range of single-strand damage types. Using this technique, we created a genome-wide map of oxidative DNA damage loci before and after repair. Oxidative lesions were heterogeneously distributed along the human genome, with less damage occurring in tight chromatin regions. Furthermore, we showed repair is prioritized for highly expressed, essential genes and in open chromatin regions. RADD-seq sheds light on cellular repair mechanisms and capable of identifying genomic hotspots prone to mutation.

scholarly journals Characteristics of mutational signatures of unknown etiology

NAR Cancer ◽  
2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Xiaoju Hu ◽  
Zhuxuan Xu ◽  
Subhajyoti De
Keyword(s):  
Dna Damage ◽  
Point Mutations ◽  
Gc Content ◽  
Unknown Origin ◽  
Unknown Etiology ◽  
Mutational Signatures ◽  
Dna Damage And Repair ◽  
Disease Etiology ◽  
Repair Processes ◽  
A Genome

Abstract Although not all somatic mutations are cancer drivers, their mutational signatures, i.e. the patterns of genomic alterations at a genome-wide scale, provide insights into past exposure to mutagens, DNA damage and repair processes. Computational deconvolution of somatic mutation patterns and expert curation pan-cancer studies have identified a number of mutational signatures associated with point mutations, dinucleotide substitutions, insertions and deletions, and rearrangements, and have established etiologies for a subset of these signatures. However, the mechanisms underlying nearly one-third of all mutational signatures are not yet understood. The signatures with established etiology and those with hitherto unknown origin appear to have some differences in strand bias, GC content and nucleotide context diversity. It is possible that some of the hitherto ‘unknown’ signatures predominantly occur outside gene regions. While nucleotide contexts might be adequate to establish etiologies of some mutational signatures, in other cases additional features, such as broader (epi)genomic contexts, including chromatin, replication timing, processivity and local mutational patterns, may help fully understand the underlying DNA damage and repair processes. Nonetheless, remarkable progress in characterization of mutational signatures has provided fundamental insights into the biology of cancer, informed disease etiology and opened up new opportunities for cancer prevention, risk management, and therapeutic decision making.

scholarly journals Virus DNA Replication and the Host DNA Damage Response

2018 ◽  
Vol 5 (1) ◽  
pp. 141-164 ◽  
Author(s):  
Matthew D. Weitzman ◽  
Amélie Fradet-Turcotte
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Life Cycles ◽  
Dynamic Interactions ◽  
Dna Damage And Repair ◽  
Dna Viruses ◽  
Cellular Processes ◽  
Damage Response ◽  
Cellular Replication ◽  
Cellular Dna

Viral DNA genomes have limited coding capacity and therefore harness cellular factors to facilitate replication of their genomes and generate progeny virions. Studies of viruses and how they interact with cellular processes have historically provided seminal insights into basic biology and disease mechanisms. The replicative life cycles of many DNA viruses have been shown to engage components of the host DNA damage and repair machinery. Viruses have evolved numerous strategies to navigate the cellular DNA damage response. By hijacking and manipulating cellular replication and repair processes, DNA viruses can selectively harness or abrogate distinct components of the cellular machinery to complete their life cycles. Here, we highlight consequences for viral replication and host genome integrity during the dynamic interactions between virus and host.

scholarly journals Mitochondrial and Nuclear DNA Damage and Repair in Age-Related Macular Degeneration

2013 ◽  
Vol 14 (2) ◽  
pp. 2996-3010 ◽  
Author(s):  
Janusz Blasiak ◽  
Sylwester Glowacki ◽  
Anu Kauppinen ◽  
Kai Kaarniranta
Keyword(s):  
Dna Damage ◽  
Macular Degeneration ◽  
Nuclear Dna ◽  
Age Related Macular Degeneration ◽  
Dna Damage And Repair ◽  
Age Related

scholarly journals Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Kinjal Majumder ◽  
Juexin Wang ◽  
Maria Boftsi ◽  
Matthew S Fuller ◽  
Jordan E Rede ◽  
...  
Keyword(s):  
Dna Damage ◽  
Virus Genome ◽  
Chromosome Conformation ◽  
Minute Virus Of Mice ◽  
Capture Assay ◽  
Genome Wide ◽  
Topologically Associated Domains ◽  
Infected Cells ◽  
Minute Virus ◽  
Cellular Dna

We have developed a generally adaptable, novel high-throughput Viral Chromosome Conformation Capture assay (V3C-seq) for use in trans that allows genome-wide identification of the direct interactions of a lytic virus genome with distinct regions of the cellular chromosome. Upon infection, we found that the parvovirus Minute Virus of Mice (MVM) genome initially associated with sites of cellular DNA damage that in mock-infected cells also exhibited DNA damage as cells progressed through S-phase. As infection proceeded, new DNA damage sites were induced, and virus subsequently also associated with these. Sites of association identified biochemically were confirmed microscopically and MVM could be targeted specifically to artificially induced sites of DNA damage. Thus, MVM established replication at cellular DNA damage sites, which provide replication and expression machinery, and as cellular DNA damage accrued, virus spread additionally to newly damaged sites to amplify infection. MVM-associated sites overlap significantly with previously identified topologically-associated domains (TADs).

scholarly journals Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis

2017 ◽  
Author(s):  
Anna R Poetsch ◽  
Simon J Boulton ◽  
Nicholas M Luscombe
Keyword(s):  
Dna Damage ◽  
Oxidative Damage ◽  
Oxidative Dna Damage ◽  
Molecular Mechanisms ◽  
Accumulation Rate ◽  
Repetitive Sequences ◽  
Open Chromatin ◽  
Regulatory Sequences ◽  
Dna Damage And Repair ◽  
A Genome

AbstractDNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well-understood, damage impact and execution of repair across a genome remains poorly defined. To bridge the gap between our understanding of DNA repair and mutation distributions we developed a novel method, AP-seq, capable of mapping apurinic sitesand 8-oxo-7,8-dihydroguanine bases at ∼300bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of oxidative damage varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike SNVs in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Oxidative damage is also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe decreased damage at promoters, exons and termination sites, but not introns, in a seemingly transcription-independent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, genes and other functional elements. Taken together, our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safe-guards the regulatory sequences and the coding regions of genes from mutations.

scholarly journals Genome-wide screening identifies cell cycle control as a synthetic lethal pathway with SRSF2P95H mutation

2021 ◽  
Author(s):  
Jane Jialu Xu ◽  
Alistair M Chalk ◽  
Iva Nikolic ◽  
Kaylene Simpson ◽  
Monique F Smeets ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Damage ◽  
Cell Lines ◽  
Dna Damage Response ◽  
Functional Screening ◽  
Wild Type ◽  
Synthetic Lethal ◽  
Genome Wide ◽  
A Genome ◽  
Damage Response

Current strategies to target RNA splicing mutant myeloid cancers proposes targeting the remaining splicing apparatus. This approach has only been modestly sensitizing and is also toxic to non-mutant bearing wild-type cells. To explore potentially exploitable genetic interactions with spliceosome mutations, we combined data mining and functional screening for synthetic lethal interactions with an Srsf2P95H/+ mutation. Analysis of mis-splicing events in a series of both human and murine SRSF2P95H mutant samples across multiple myeloid diseases (AML, MDS, CMML) was performed to identify conserved mis-splicing events. From this analysis, we identified that the cell cycle and DNA repair pathways were overrepresented within the conserved mis-spliced transcript sets. In parallel, to functionally define pathways essential for survival and proliferation of Srsf2P95H/+ cells, we performed a genome-wide CRISPR loss of function screen using Hoxb8 immortalized R26-CreERki/+ Srsf2P95H/+ and R26-CreERki/+ Srsf2+/+ cell lines. We assessed loss of sgRNA representation at three timepoints: immediately after Srsf2P95H/+ activation, and at one week and two weeks post Srsf2P95H/+ mutation. Pathway analysis demonstrated that the cell cycle and DNA damage response pathways were amongst the top synthetic lethal pathways with Srsf2P95H/+ mutation. Based on the loss of guide RNAs targeting Cdk6, we identified that Palbociclib, a CDK6 inhibitor, showed preferential sensitivity in Srsf2P95H/+ cell lines and in primary non-immortalized lin-cKIT+Sca-1+ cells compared to wild type controls. Our data strongly suggest that the cell cycle and DNA damage response pathways are required for Srsf2P95H/+ cell survival, and that Palbociclib could be an alternative therapeutic option for targeting SRSF2 mutant cancers.

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