Article
Multidisciplinary Sciences
Zhiqian Li, Nimi Marcel, Sushil Devkota, Ankush Auradkar, Stephen M. Hedrick, Valentino M. Gantz, Ethan Bier
Summary: Research in Drosophila has shown that inserting CopyCatcher systems can efficiently detect somatic gene conversion events, revealing unexpectedly high rates of SGC; through RNAi genetic screening, several new loci that affect SGC efficiency have been identified, including c-MYC.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Megumi Ishii, Tetsuya Ishii
Summary: This passage discusses whether genome-edited agricultural products should be considered genetically modified organisms (GMOs) and how to prove definitively that a genome-edited organism does not contain exogenous DNA, taking social aspects into account.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Ali Abu Shqair, Ui-Seob Lee, Eun-Hee Kim
Summary: In cellular experiments, a practical modelling has been developed to simulate the occurrences of double-strand breaks (DSBs) and the formations of gamma-H2AX foci in response to individual DSB formations, in cell nucleus due to exposure to alpha particles. This computational modelling can better implement the conventional gamma-H2AX assay.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Laure Bobyk, Francois Vianna, Juan S. Martinez, Gaetan Gruel, Marc Benderitter, Celine Baldeyron
Summary: In this study, we investigated the dynamics of DNA repair pathways in response to alpha-particle irradiation, and found that different mechanisms are recruited at DNA damage sites. This research is important for assessing the risk associated with radiation exposure and improving the efficacy of radiation treatment.
Article
Multidisciplinary Sciences
Jakub Wiktor, Arvid H. Gynna, Prune Leroy, Jimmy Larsson, Giovanna Coceano, Ilaria Testa, Johan Elf
Summary: Homologous recombination is crucial for accurate DNA repair, with repair of double-stranded DNA breaks in E. coli completed in approximately 15 minutes. The search for homologous repair templates takes less than 9 minutes and is mediated by a thin and highly dynamic RecA filament stretching throughout the cell. This model effectively reduces search dimensionality, with search time consistent across different cell lengths and DNA amounts.
Article
Cell Biology
Juliette Dabin, Margherita Mori, Sophie E. Polo
Summary: This review summarizes recent advances in understanding the coordination between chromatin maintenance and the DNA damage response (DDR) in the cell nucleus. The authors discuss how the DDR affects chromatin marks, organization, and mobility, and how chromatin alterations contribute to the DDR. They also present current knowledge of the molecular mechanisms underlying these processes in physiological and pathological conditions, and highlight unanswered questions in this field.
CURRENT OPINION IN CELL BIOLOGY
(2023)
Article
Biology
Nadia Vertti-Quintero, Ethan Levien, Lucie Poggi, Ariel Amir, Guy-Franck Richard, Charles N. N. Baroud
Summary: This study demonstrates the use of microfluidic device to study DSBR at a single-cell level in yeast. The dynamics of DSBR were analyzed and a differential equation model was developed to obtain repair process rates. The study identified three types of DSB repair events that were previously unrecognized.
Article
Biochemistry & Molecular Biology
Ioannis Emmanouilidis, Natalia Fili, Alexander W. Cook, Yukti Hari-Gupta, Alia dos Santos, Lin Wang, Marisa L. Martin-Fernandez, Peter J. I. Ellis, Christopher P. Toseland
Summary: Mammalian cells are constantly exposed to various DNA damaging events, leading to the activation of DNA repair pathways. Cas9-based genomic intervention allows for induced DSBs at defined quantities and locations across the human genome, utilizing custom-designed promiscuous guide RNAs based on in silico predictions. This provides a generic, low-cost, and rapid methodology for inducing controlled DNA damage in cell culture models.
Review
Biochemistry & Molecular Biology
Matvey Mikhailovich Murashko, Ekaterina Mikhailovna Stasevich, Anton Markovich Schwartz, Dmitriy Vladimirovich Kuprash, Aksinya Nicolaevna Uvarova, Denis Eriksonovich Demin
Summary: Incorrect repair of DNA double-strand breaks leading to chromosomal rearrangements is a major cause of oncogenesis. Recent studies have highlighted the key role of various types of RNA in the formation, recognition, and repair of DSBs, with gene mutations or changes in RNA expression levels potentially leading to DNA repair defects and increased chromosome aberration frequency. Additionally, certain RNAs have been shown to stimulate long-range chromosomal rearrangements, and further research is needed to understand how RNA mediates specific chromosomal rearrangements.
Article
Chemistry, Multidisciplinary
Deepak J. Prabhu, Ujjayinee Ray, Anjaly Rajeev, Reshma Joy, Abi Thoppilan George, Jinu George, Sathees C. Raghavan, Franklin John
Summary: A new multicomponent reaction involving sulfonamide-conjugated ketenimines is reported. The reaction is atom economical and stereoselective, generating key intermediates for further synthesis of compounds. The synthesized molecules exhibit potential for targeting the NHEJ pathway and have cytotoxic abilities. Computational studies and in vitro biological assays support the findings.
Article
Multidisciplinary Sciences
Ye Cai, Huifen Cao, Fang Wang, Yufei Zhang, Philipp Kapranov
Summary: This study presents a high-resolution method, SSiNGLe-AP, to map abasic (AP) sites in mammalian genomes. The results show that AP sites are nonrandomly distributed in the genome and are influenced by gene expression, age, and tissue type.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Rizky Mutiara Fatimah, Nikko Adhitama, Yasuhiko Kato, Hajime Watanabe
Summary: In this study, a transgenic D. magna line was developed and a reporter gene system expressing mCherry and eGFP was established using CRISPR/Cas technology to evaluate homology-directed repair (HDR). This system can expand our understanding of HDR mechanisms and improve the HDR-based gene-editing system in this species.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Anika Kuster, Nour L. Mozaffari, Oliver J. Wilkinson, Jessica L. Wojtaszek, Christina Zurfluh, Sara Przetocka, Dawid Zyla, Christine von Aesch, Mark S. Dillingham, R. Scott Williams, Alessandro A. Sartori
Summary: A peptide mimetic targeting CtIP was developed, which effectively inhibits CtIP activity, leading to impaired DNA repair and replication fork degradation, with selective toxicity to BRCA1-mutated cancer cells. This study provides a theoretical basis for the future development of CtIP-targeting compounds for cancer treatment.
Article
Biochemistry & Molecular Biology
Sahar Waseem, Sudeep Kumar, Kanghoon Lee, Byoung-Ha Yoon, Mirang Kim, Hail Kim, Keesook Lee
Summary: PRMT1 is crucial for male fertility in mice, as its deficiency leads to impaired repair pathway of DNA double-strand breaks in male germ cells. This study provides new insight into the role of PRMT1-mediated asymmetric demethylation in mouse spermatogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Shan Huang, Kaihang Wang, Stephen L. Mayo
Summary: A recent study shows that CbAgo, a prokaryotic argonaute, can induce DNA interference and generate double-stranded breaks in target DNAs. The study demonstrates that CbAgo can cleave genome target sites and induce chromosome recombination in Escherichia coli. The findings suggest that the guide-directed cleavage of pAgo on the host genome is mutagenic and can be utilized in genetic manipulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Kyung-Jong Lee, Janapriya Saha, Jingxin Sun, Kazi R. Fattah, Shu-Chi Wang, Burkhard Jakob, Linfeng Chi, Shih-Ya Wang, Gisela Taucher-Scholz, Anthony J. Davis, David J. Chen
NUCLEIC ACIDS RESEARCH
(2016)
Article
Multidisciplinary Sciences
Xue-Song Liu, Gurushankar Chandramouly, Emilie Rass, Yinghua Guan, Guocan Wang, Robin M. Hobbs, Anbazhagan Rajendran, Anyong Xie, Jagesh V. Shah, Anthony J. Davis, Ralph Scully, Andrea Lunardi, Pier Paolo Pandolfi
NATURE COMMUNICATIONS
(2015)
Article
Biochemistry & Molecular Biology
Eiichiro Mori, Anthony J. Davis, Masatoshi Hasegawa, David J. Chen
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2016)
Article
Biology
Janapriya Saha, Anthony J. Davis
JOURNAL OF RADIATION RESEARCH
(2016)
Article
Multidisciplinary Sciences
Huiming Lu, Raghavendra A. Shamanna, Jessica K. de Freitas, Mustafa Okur, Prabhat Khadka, Tomasz Kulikowicz, Priscella P. Holland, Jane Tian, Deborah L. Croteau, Anthony J. Davis, Vilhelm A. Bohr
NATURE COMMUNICATIONS
(2017)
Review
Oncology
Osama Mohamad, Brock J. Sishc, Janapriya Saha, Arnold Pompos, Asal Rahimi, Michael D. Story, Anthony J. Davis, D. W. Nathan Kim
Review
Oncology
Brock J. Sishc, Anthony J. Davis
Article
Oncology
Brandt A. Nichols, Nathaniel W. Oswald, Elizabeth A. McMillan, Kathleen McGlynn, Jingsheng Yan, Min S. Kim, Janapriya Saha, Prema L. Mallipeddi, Sydnie A. LaDuke, Pamela A. Villalobos, Jaime Rodriguez-Canales, Ignacio I. Wistuba, Bruce A. Posner, Anthony J. Davis, John D. Minna, John B. MacMillan, Angelique W. Whitehurst
Article
Biochemistry & Molecular Biology
Anthony J. Davis, Linfeng Chi, Sairei So, Kyung-Jong Lee, Eiichiro Mori, Kazi Fattah, Jun Yang, David J. Chen
NUCLEIC ACIDS RESEARCH
(2014)
Article
Biochemistry & Molecular Biology
Huiming Lu, Janapriya Saha, Pauline J. Beckmann, Eric A. Hendrickson, Anthony J. Davis
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Janapriya Saha, Jinsung Bae, Shih-Ya Wang, Huiming Lu, Lori J. Chappell, Purva Gopal, Anthony J. Davis
Summary: The study found that mutating putative Ku70 phosphorylation sites results in defective DNA damage repair, leading to genomic instability and accelerated development of HCC.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Huiming Lu, Junhong Guan, Shih-Ya Wang, Guo-Min Li, Vilhelm A. Bohr, Anthony J. Davis
Summary: RECQL4 promotes the stabilization of NHEJ machinery at DSBs to support repair. The kinase activity of DNA-PKcs is required for the accumulation of RECQL4 to DSBs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Huiming Lu, Qin Zhang, Daniel J. Laverty, Andrew C. Puncheon, Mathew M. Augustine, Gareth J. Williams, Zachary D. Nagel, Benjamin P. C. Chen, Anthony J. Davis
Summary: In this study, it was found that ATM drives the DNA damage response by modulating multiple signal transduction and DNA repair pathways. ATM phosphorylates DNA-PKcs at threonine 4102 (T4102) in response to DSBs, promoting NHEJ-dependent repair and increasing genomic stability. These findings highlight the key role of ATM in DNA repair.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Luis Reza Herrera, Ronnesha A. Johnson, Kathleen McGlynn, Zane A. Gibbs, Anthony J. Davis, Angelique W. Whitehurst
Summary: Tumor-induced expression of meiotic genes, particularly HORMAD1, is associated with reduced patient survival and increased genomic instability. HORMAD1 plays a critical role in protecting stalled DNA replication forks and preventing DNA strand degradation. Loss of HORMAD1 leads to increased DNA breaks and chromosomal defects, exacerbated by induction of replication stress.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)