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Nature Reviews. Genetics May 2024Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost... (Review)
Review
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology.
Topics: DNA Repair; Phylogeny; Homologous Recombination; Meiosis; DNA Breaks, Double-Stranded
PubMed: 38036793
DOI: 10.1038/s41576-023-00669-8 -
Nature Communications Jan 2024The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic...
The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates the completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus-specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.
Topics: Animals; DNA Repair; Excision Repair; Poly ADP Ribosylation; DNA Demethylation; Proteomics; Poly (ADP-Ribose) Polymerase-1; DNA Damage; DNA; Mammals
PubMed: 38167803
DOI: 10.1038/s41467-023-44209-8 -
Cell Reports May 2024Innovative methods to retrieve proteins associated with actively replicating DNA have provided a glimpse into the molecular dynamics of replication fork stalling. We...
Innovative methods to retrieve proteins associated with actively replicating DNA have provided a glimpse into the molecular dynamics of replication fork stalling. We report that a combination of density-based replisome enrichment by isolating proteins on nascent DNA (iPOND2) and label-free quantitative mass spectrometry (iPOND2-DRIPPER) substantially increases both replication factor yields and the dynamic range of protein quantification. Replication protein abundance in retrieved nascent DNA is elevated up to 300-fold over post-replicative controls, and recruitment of replication stress factors upon fork stalling is observed at similar levels. The increased sensitivity of iPOND2-DRIPPER permits direct measurement of ubiquitination events without intervening retrieval of diglycine tryptic fragments of ubiquitin. Using this approach, we find that stalled replisomes stimulate the recruitment of a diverse cohort of DNA repair factors, including those associated with poly-K63-ubiquitination. Finally, we uncover the temporally controlled association of stalled replisomes with nuclear pore complex components and nuclear cytoskeleton networks.
Topics: DNA Replication; Humans; Ubiquitination; DNA Repair; DNA
PubMed: 38703364
DOI: 10.1016/j.celrep.2024.114178 -
Diabetic Medicine : a Journal of the... Jan 2024Diabetes is a chronic disorder with rapidly increasing prevalence that is a major global issue of our current era. There are two major types of diabetes. Polygenic forms... (Review)
Review
Diabetes is a chronic disorder with rapidly increasing prevalence that is a major global issue of our current era. There are two major types of diabetes. Polygenic forms of diabetes include type 1 diabetes (T1D) and type 2 diabetes (T2D) and its monogenic forms are maturity-onset diabetes of the young (MODY) and neonatal diabetes mellitus (NDM). There are no permanent therapeutic approaches for diabetes and current therapies rely on regular administration of various drugs or insulin injection. Recently, gene editing strategies have offered new promise for treating genetic disorders. Targeted genome editing is a fast-growing technology, recruiting programmable nucleases to specifically modify target genomic sequences. These targeted nucleases generate double-strand breaks at target regions in the genome, which induce cellular repair pathways including non-homologous end joining (NHEJ) and homology-directed repair (HDR). Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a novel gene-editing system, permitting precise genome modification. CRISPR/Cas9 has great potential for various applications in diabetic research such as gene screening, generation of diabetic animal models and treatment. In this article, gene-editing strategies are summarized with a focus on the CRISPR/Cas9 approach in diabetes research.
Topics: Animals; CRISPR-Cas Systems; Diabetes Mellitus, Type 2; Gene Editing; Recombinational DNA Repair; DNA End-Joining Repair
PubMed: 37833064
DOI: 10.1111/dme.15240 -
Cancer Biology & Therapy Dec 2023Hepatocellular carcinoma (HCC) is one of the most common types of malignant tumors with increasing incidence rates and high mortality rates. The currently available...
Hepatocellular carcinoma (HCC) is one of the most common types of malignant tumors with increasing incidence rates and high mortality rates. The currently available methods for treating HCC include surgery, radiotherapy or chemotherapy, but all of them have limitations. Therefore, developing novel therapeutic methods for HCC is in great need. Here, in this study, we found that tanshinone I, a small molecule compound, inhibited the proliferation of HCC cells in a dose-dependent manner. We also observed that Tanshinone I destabilized genomes by inhibiting both NHEJ and HR repair pathways, which are responsible for repairing DNA double strand breaks (DSBs). Mechanistically, this compound suppressed the expression of 53BP1, and the recruitment of RPA2 to DNA damage sites. Importantly, we demonstrated that combining Tanshinone I with radiotherapy exhibited better therapeutic potential for treating HCC.
Topics: Humans; DNA Breaks, Double-Stranded; Carcinoma, Hepatocellular; Liver Neoplasms; DNA Repair; DNA; DNA End-Joining Repair; Recombinational DNA Repair
PubMed: 37408176
DOI: 10.1080/15384047.2023.2229958 -
DNA Repair Sep 2023The perturbation of DNA replication, a phenomena termed "replication stress", is a driving force of genome instability and a hallmark of cancer cells. Among the DNA... (Review)
Review
The perturbation of DNA replication, a phenomena termed "replication stress", is a driving force of genome instability and a hallmark of cancer cells. Among the DNA repair mechanisms that contribute to tolerating replication stress, the homologous recombination pathway is central to the alteration of replication fork progression. In many organisms, defects in the homologous recombination machinery result in increased cell sensitivity to replication-blocking agents and a higher risk of cancer in humans. Moreover, the status of homologous recombination in cancer cells often correlates with the efficacy of anti-cancer treatment. In this review, we discuss our current understanding of the different functions of homologous recombination in fixing replication-associated DNA damage and contributing to complete genome duplication. We also examine which functions are pivotal in preventing cancer and genome instability.
Topics: Humans; DNA Replication; DNA Damage; Homologous Recombination; DNA Repair; Genomic Instability
PubMed: 37541027
DOI: 10.1016/j.dnarep.2023.103548 -
Nature Communications Feb 2024Drugs targeting the DNA damage response (DDR) are widely used in cancer therapy, but resistance to these drugs remains a major clinical challenge. Here, we show that...
Drugs targeting the DNA damage response (DDR) are widely used in cancer therapy, but resistance to these drugs remains a major clinical challenge. Here, we show that SYCP2, a meiotic protein in the synaptonemal complex, is aberrantly and commonly expressed in breast and ovarian cancers and associated with broad resistance to DDR drugs. Mechanistically, SYCP2 enhances the repair of DNA double-strand breaks (DSBs) through transcription-coupled homologous recombination (TC-HR). SYCP2 promotes R-loop formation at DSBs and facilitates RAD51 recruitment independently of BRCA1. SYCP2 loss impairs RAD51 localization, reduces TC-HR, and renders tumors sensitive to PARP and topoisomerase I (TOP1) inhibitors. Furthermore, our studies of two clinical cohorts find that SYCP2 overexpression correlates with breast cancer resistance to antibody-conjugated TOP1 inhibitor and ovarian cancer resistance to platinum treatment. Collectively, our data suggest that SYCP2 confers cancer cell resistance to DNA-damaging agents by stimulating R-loop-mediated DSB repair, offering opportunities to improve DDR therapy.
Topics: R-Loop Structures; DNA Repair; DNA Breaks, Double-Stranded; Homologous Recombination; BRCA1 Protein; DNA; Rad51 Recombinase; Recombinational DNA Repair
PubMed: 38383600
DOI: 10.1038/s41467-024-45693-2 -
International Journal of Molecular... Aug 2023The critical role of the DNA repair system in preserving the health and survival of living organisms is widely recognized as dysfunction within this system can result in... (Review)
Review
The critical role of the DNA repair system in preserving the health and survival of living organisms is widely recognized as dysfunction within this system can result in a broad range of severe conditions, including neurodegenerative diseases, blood disorders, infertility, and cancer. Despite comprehensive research on the molecular and cellular mechanisms of DNA repair pathways, there remains a significant knowledge gap concerning these processes at an organismal level. The teleost zebrafish has emerged as a powerful model organism for investigating these intricate DNA repair mechanisms. Their utility arises from a combination of their well-characterized genomic information, the ability to visualize specific phenotype outcomes in distinct cells and tissues, and the availability of diverse genetic experimental approaches. In this review, we provide an in-depth overview of recent advancements in our understanding of the in vivo roles of DNA repair pathways. We cover a variety of critical biological processes including neurogenesis, hematopoiesis, germ cell development, tumorigenesis, and aging, with a specific emphasis on findings obtained from the use of zebrafish as a model system. Our comprehensive review highlights the importance of zebrafish in enhancing our understanding of the functions of DNA repair systems at the organismal level and paves the way for future investigations in this field.
Topics: Animals; Zebrafish; Aging; Carcinogenesis; Cell Differentiation; DNA Repair
PubMed: 37685935
DOI: 10.3390/ijms241713120 -
Environmental Pollution (Barking, Essex... Dec 2023Bacteria thriving in the mangrove ecosystem are major drivers of elemental cycles. Climate change and environmental stressors (heavy metals) influence the performance of... (Review)
Review
Bacteria thriving in the mangrove ecosystem are major drivers of elemental cycles. Climate change and environmental stressors (heavy metals) influence the performance of these microorganisms, thereby affecting the biogeochemical cycle. The present study reports the genotoxic effect of climatic and heavy metal stressors on mangrove bacteria and their adaptation strategies. Comparative analysis between two bacterial strains, Bacillus stercoris GST-03 and Pseudomonas balearica DST-02 isolated from the Bhitarkanika mangrove ecosystem, Odisha, India, showed cellular injuries in response to various stressors as evident by declined growth, elevated levels of reactive oxygen species (ROS) and resulted DNA damage. B. stercoris GST-03 showed more tolerance towards acidic pH, whereas P. balearica DST-02 showed higher tolerance towards UV exposure and heavy metals (Lead and Cadmium). The adaptation strategies of the strains revealed a significant role of GST in ROS scavenging activity and the involvement of Nucleotide excision repair or SOS response pathways. However, irreparable DNA damage was observed at pH 9 and 200 ppm Cd in B. stercoris GST-03, and at pH 4, 1000 ppm of Pb and 200 ppm of Cd in P. balearica DST-02. The current findings provide a broad overview of bacterial response and adaptability concerning future climate and environmental changes.
Topics: Bacteria; Cadmium; DNA Damage; DNA Repair; Ecosystem; Metals, Heavy; Oxidative Stress; Reactive Oxygen Species
PubMed: 37863253
DOI: 10.1016/j.envpol.2023.122722 -
DNA Repair Sep 2023The human genome is continually exposed to various stressors, which can result in DNA damage, mutations, and diseases. Among the different types of DNA damage,... (Review)
Review
The human genome is continually exposed to various stressors, which can result in DNA damage, mutations, and diseases. Among the different types of DNA damage, single-strand lesions are commonly induced by external stressors and metabolic processes. Accurate detection and quantification of DNA damage are crucial for understanding repair mechanisms, assessing environmental impacts, and evaluating response to therapy. However, traditional techniques have limitations in sensitivity and the ability to detect multiple types of damage. In recent years, single-molecule fluorescence approaches have emerged as powerful tools for precisely localizing and quantifying DNA damage. Repair Assisted Damage Detection (RADD) is a single-molecule technique that employs specific repair enzymes to excise damaged bases and incorporates fluorescently labeled nucleotides to visualize the damage. This technique provides valuable insights into repair efficiency and sequence-specific damage. In this review, we discuss the principles and applications of RADD assays, highlighting their potential for enhancing our understanding of DNA damage and repair processes.
Topics: Humans; DNA Repair; DNA Damage
PubMed: 37467630
DOI: 10.1016/j.dnarep.2023.103533