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
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.
Review
Genetics & Heredity
Bert van de Kooij, Haico van Attikum
Summary: The repair of DNA double-strand breaks plays a crucial role in maintaining genome integrity. Various pathways can repair the breaks, leading to either error-free or highly mutagenic outcomes. Genomic reporter constructs have been used extensively to study this process, allowing researchers to quantifiably assess repair by measuring the expression of fluorescent proteins. Recent advancements in genome editing technologies, such as CRISPR-Cas9, have further enhanced the utility of reporter constructs. In this review, the available DNA double-strand break repair pathway reporters will be discussed and compared, with considerations for choosing the appropriate reporter and future prospects in this field.
FRONTIERS IN GENETICS
(2022)
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
Biochemistry & Molecular Biology
Dipayan Ghosh, Susmita Kumari, Sathees C. Raghavan
Summary: The study investigates the functional role of RNASEH2A and RNASEH2B in leukemic cells and finds that they affect cell survival and apoptosis. Knockdown of RNASEH2A or RNASEH2B also leads to cell cycle arrest at the S phase and increases the difficulty of DNA repair.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
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.
Review
Genetics & Heredity
Alice Libri, Timea Marton, Ludovic Deriano
Summary: DNA double-strand breaks are highly toxic and can be repaired via multiple DNA repair pathways. During V(D)J recombination, certain parameters restrict the repair of DSBs to the non-homologous end-joining pathway.
FRONTIERS IN GENETICS
(2022)
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
Biochemistry & Molecular Biology
Su Hyung Park, Namwoo Kim, Nalae Kang, Eunjin Ryu, Eun A. Lee, Jae Sun Ra, Anton Gartner, Sukhyun Kang, Kyungjae Myung, Kyoo-young Lee
Summary: This study reveals the important role of ATAD5 in short-range end resection and highlights the critical role of PCNA regulation at DSB in proper DNA repair and HR.
NUCLEIC ACIDS RESEARCH
(2023)
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)