Article
Multidisciplinary Sciences
Osama Garwain, Xiaoming Sun, Divya Ramalingam Iyer, Rui Li, Lihua Julie Zhu, Paul D. Kaufman
Summary: The depletion of Ki-67 in vertebrate mammals can cause DNA damage, particularly in mitotic cells. The C-terminal chromatin-binding domain of Ki-67 plays a crucial role in protecting cells from this damage. Simultaneous depletion of Ki-67 and p53 results in increased chromosome bridges and micronuclei, highlighting the importance of Ki-67 in maintaining genome stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Medicine, Research & Experimental
Qing Yin, Ya-Jie Zhao, Wei-Jie Ni, Tao-Tao Tang, Yao Wang, Jing-Yuan Cao, Di Yin, Yi Wen, Zuo-Lin Li, Yi-Lin Zhang, Wei Jiang, Yue Zhang, Xiao-Yu Lu, Ai-Qing Zhang, Wei-Hua Gan, Lin-Li Lv, Bi-Cheng Liu, Bin Wang
Summary: This study found that miR-155 overexpression was associated with cisplatin-induced acute kidney injury (cAKI), and inhibition of miR-155 expression could attenuate cAKI-induced renal damage and apoptosis. The study also revealed that miR-155 inhibition increased the expression of TRF1 and CDK12, thereby limiting telomeric dysfunction and genomic DNA damage.
Editorial Material
Genetics & Heredity
Yang Zheng, Hao Li, Xiaochen Bo, Hebing Chen
Summary: Ionizing radiation (IR) induces complex DNA damage and repair mechanisms at hierarchical chromatin structures, necessitating the study of radiobiology from a 3D-genomic perspective. Differences in IR damage and repair within the 3D genome may provide insights into variations in radiosensitivity.
TRENDS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Ulysses Tsz Fung Lam, Ee Sin Chen
Summary: SETD2 serves as a critical tumor suppressor in governing genomic stability, DNA damage response, and cell cycle progression. Mutations in SETD2 may play a significant role in tumorigenesis and also represent a potential target in precision cancer therapy.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2022)
Article
Biochemical Research Methods
Erfaneh Gharavi, Aaron Gu, Guangtao Zheng, Jason P. Smith, Hyun Jae Cho, Aidong Zhang, Donald E. Brown, Nathan C. Sheffield
Summary: The study introduces a new method of representing genomic region sets as vectors using word2vec, reducing dimensionality to 100 without significant loss in classification performance. The vector representation can accurately identify cell line, antibody, and tissue type, and is more robust when summarizing simulated random perturbations and subsampling data derived from different peak calling thresholds. The evaluations show that the vectors retain useful biological information in relatively lower-dimensional spaces, suggesting that vector representation of region sets is a promising approach for efficient analysis of genomic region data.
Article
Cell Biology
Josephine Groslambert, Evgeniia Prokhorova, Anne R. Wondisford, Callum Tromans-Coia, Celeste Giansanti, Jennifer Jansen, Gyula Timinszky, Matthias Dobbelstein, Dragana Ahel, Roderick J. O'Sullivan, Ivan Ahel
Summary: This study reveals the crucial role of ADP-ribose hydrolase TARG1 in DNA repair and the DNA damage response, as well as its interaction with other enzymes such as PARG, which is important for maintaining genome stability.
Article
Biochemistry & Molecular Biology
Hadar Golan Berman, Pooja Chauhan, Shira Shalev, Hiba Hassanain, Avital Parnas, Sheera Adar
Summary: The study identified that in a specific cell line system, cisplatin resistant cells had less damage but similar repair kinetics. Through mapping gene expression changes, 56 upregulated genes were identified that could potentially impact the response to cisplatin.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Yiming Qiu, Xianping Xie, Luhua Lin
Summary: This study identified that circFOXO3 protects cardiomyocytes from radiation-induced cardiotoxicity by reducing DNA damage and apoptosis, suggesting circFOXO3 could be a potential therapeutic target against radiation-induced cardiotoxicity.
MOLECULAR MEDICINE REPORTS
(2021)
Review
Cell Biology
John M. M. Danforth, Luc Provencher, Aaron A. A. Goodarzi
Summary: Exposure to environmental ionizing radiation, particularly high-LET radiation, can induce clustered DNA damage that is challenging to repair. Understanding the role of chromatin in the repair process is essential for assessing the effects of radiation exposure.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Pharmacology & Pharmacy
Qingwen Yuan, Renjun Peng, Huijie Yu, Sinian Wang, Zhongmin Chen, Suhe Dong, Wei Li, Bo Cheng, Qisheng Jiang, Yuwen Cong, Fengsheng Li, Changzheng Li
Summary: The study demonstrates that disulfiram, an FDA-approved alcohol deterrent, shows radioprotective efficacy by affecting the cell cycle and regulating the DNA damage response and survival of intestinal stem cells. It could be a promising candidate for preventing radiation-induced intestinal injury (RIII) in cancer therapy and nuclear accidents.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Multidisciplinary Sciences
Kader Salifou, Callum Burnard, Poornima Basavarajaiah, Giuseppa Grasso, Marion Helsmoortel, Victor Mac, David Depierre, Celine Franckhauser, Emmanuelle Beyne, Xavier Contreras, Jerome Dejardin, Sylvie Rouquier, Olivier Cuvier, Rosemary Kiernan
Summary: MRN-MDC1 plays a central role in DNA damage response and repair, interacting with factors involved in gene expression and RNA processing, as well as DDR factors. Association of MRN with the transcriptional machinery scans active genes for transcription-induced DNA damage to preserve genome integrity.
Article
Biochemistry & Molecular Biology
Lei Tian, Niannian Ding, Xuehui Liu, Yuanyuan Chen, Zhenfeng Zhang
Summary: This study analyzed the critical role of F41 in protein folding of Cren7. Mutation analysis revealed that the mutation of F41 led to misfolding and reduced stability of Cren7, but had minimal effect on the activities of DNA binding and supercoiling. Furthermore, F41A lost the ability to form oligomers/polymers on DNA.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Parviz Seifpanahi Shabane, Alexey Onufriev
Summary: The study explores the conformational changes of the H4 tail under different charged states. As the charge of the H4 tail is gradually neutralized, its structure transitions from a random coil to a more compact and stable form. Based on ensemble similarity, K -> M is proposed as a possible alternative to the commonly used K -> Q substitution.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Cell Biology
Isabelle Trier, Elizabeth M. Black, Yoon Ki Joo, Lilian Kabeche
Summary: We have found that ATR kinase, a master regulator of the DNA damage response, protects CENP-A protein occupancy at centromeres during interphase independent of DNA damage. Furthermore, ATR-dependent phosphorylation of DAXX protein regulates CENP-A occupancy at centromeres and DAXX localization. Lastly, acute ATR inhibition during interphase leads to kinetochore formation defects and an increased rate of lagging chromosomes. These findings highlight a mechanism by which ATR protects centromere identity and genome stability.
Article
Multidisciplinary Sciences
Takashi Nishio, Yuko Yoshikawa, Kenichi Yoshikawa, Shin-ichi Sato
Summary: This study demonstrates that longer DNA molecules exhibit significantly greater potency in cell-free gene expression, potentially due to the favorable access of RNA polymerase to shrunken DNA conformation. This finding provides a new perspective on the regulatory mechanisms of gene expression.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Satoru Ide, Sachiko Tamura, Kazuhiro Maeshima
Summary: The chromatin, consisting of nucleosomes and associated proteins and RNAs, plays a critical role in regulating genome functions. Single-nucleosome imaging is an effective method to investigate the behavior of chromatin in living cells, providing insights into its organization and dynamics not observed in fixed cells. Analyzing the motion data from various aspects can contribute to a better understanding of genome functions.
Article
Biochemistry & Molecular Biology
Marcos K. Masukawa, Yusuke Sato, Fujio Yu, Kanta Tsumoto, Kenichi Yoshikawa, Masahiro Takinoue
Summary: This paper describes a purification method based on water-in-water droplet fractionation for separating excess components from self-assembled DNA nano/microstructures. The method is cost-effective and simple, and allows purification of structures with a broad size spectrum.
Editorial Material
Multidisciplinary Sciences
Kazuhiro Maeshima
Article
Multidisciplinary Sciences
Shiori Iida, Soya Shinkai, Yuji Itoh, Sachiko Tamura, Masato T. Kanemaki, Shuichi Onami, Kazuhiro Maeshima
Summary: The study revealed that local chromatin motion remains steady in live human cells throughout the phases of G1, S, and G2, driven mainly by thermal fluctuations, with an increase in motion following a DNA damage response. These findings support the viscoelastic properties of chromatin and suggest that steady-state chromatin motion enables cells to perform housekeeping functions during interphase.
Editorial Material
Cell Biology
Kazuhiro Maeshima, Eran Meshorer
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Materials Science, Biomaterials
Takashi Nishio, Tomoya Masaoka, Yuko Yoshikawa, Koichiro Sadakane, Takahiro Kenmotsu, Helmut Schiessel, Kenichi Yoshikawa
Summary: The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system was studied using a luciferase assay. Rb+ was found to be the most efficient in promoting TX-TL, while Li+, Na+, and (CH3)(4)N+ exhibited inhibitory effects. Similar promotion/inhibition effects were observed in cell-free translation alone using an mRNA template.
Article
Biochemistry & Molecular Biology
Jekaterina Erenpreisa, Alessandro Giuliani, Kenichi Yoshikawa, Martin Falk, Georg Hildenbrand, Kristine Salmina, Talivaldis Freivalds, Ninel Vainshelbaum, Jonas Weidner, Aaron Sievers, Gotz Pilarczyk, Michael Hausmann
Summary: Complex functioning of the genome in the cell nucleus is controlled at different levels, including the DNA base sequence, epigenetic pathways, and genome architecture. This article reviews recent research on integrating these levels of genome expression regulation and discusses the conclusions from an international symposium held in Riga, Latvia, which addressed novel aspects of the topic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Polymer Science
Kohei Fujino, Takashi Nishio, Keita Fujioka, Yuko Yoshikawa, Takahiro Kenmotsu, Kenichi Yoshikawa
Summary: This report investigates the effects of alcohols on gene expression and the mechanical properties of DNA molecules. It shows that ethanol and 2-propanol significantly increase gene expression levels, while 1-propanol has an inhibitory effect. The observation of single DNA molecules reveals that 1-propanol greatly enhances the mechanical properties of DNA, while ethanol and 2-propanol have weaker effects. These findings demonstrate a correlation between the activation/inhibition effects of alcohol isomers on gene expression and the viscoelastic properties of DNA molecules.
Article
Biochemistry & Molecular Biology
Takashi Nishio, Yohji Shimada, Yuko Yoshikawa, Takahiro Kenmotsu, Helmut Schiessel, Kenichi Yoshikawa
Summary: In this study, we used an in vitro cell-free system with spermine to investigate the effect of daunomycin (DM) on gene expression. We found that DM exhibits a bimodal effect on gene expression, promoting at lower concentrations and inhibiting at higher concentrations. Through atomic force microscopy observation, we observed that DM destroys flower-like conformations of DNA induced by spermine, resulting in double-strand breaks. These newly revealed effects of DM on gene expression and DNA structure will contribute to the development and refinement of anticancer therapy chemicals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Multidisciplinary
Maho Kuroda, Satoshi Takatori, Takahiro Kenmotsu, Kenichi Yoshikawa, Chwen-Yang Shew
Summary: Macroscopic systems mimicking microscopic systems were used to study the organization of macro-molecules in a confined space. Experimental and numerical models showed that the behavior of a large particle interacting with small particles under different boundary conditions is influenced by crowding. Membrane stiffness was found to affect the organization of biopolymers and may play a role in cellular dynamics.
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN
(2023)
Article
Chemistry, Multidisciplinary
Mayu Shono, Gen Honda, Miho Yanagisawa, Kenichi Yoshikawa, Akihisa Shioi
Summary: In this study, a one-step method using glass capillaries and a polymer blend of PEG and gelatin is discussed for producing uniform cell-sized microgels. The method involves phase separation and gelation of the polymer blend upon decreasing temperature, leading to the formation of linearly aligned, uniformly sized gelatin microgels. The addition of DNA prevents coalescence of the microdroplets. This novel method has potential applications in biopolymers and cellular models.
Article
Multidisciplinary Sciences
Tadasu Nozaki, Soya Shinkai, Satoru Ide, Koichi Higashi, Sachiko Tamura, Masa A. Shimazoe, Masaki Nakagawa, Yutaka Suzuki, Yasushi Okada, Masaki Sasai, Shuichi Onami, Ken Kurokawa, Shiori Iida, Kazuhiro Maeshima
Summary: In eukaryotes, the physical nature of higher-order chromatin organization in living cells, such as whether it is condensed or extended and whether it is liquid-like or solid-like, remains unclear. In this study, novel approaches combining genomics, single-nucleosome imaging, and computational modeling were used to investigate the physical organization and behavior of early DNA replicated regions in human cells. The results showed that nucleosomes form physically condensed domains with approximately 150-nm diameters, even in active chromatin regions. The behavior of nucleosomes within these domains is liquid-like on the scale of 150 nm/0.5 s, facilitating chromatin accessibility, while at larger scales, chromatin behaves more like a solid, potentially contributing to genome integrity.
Article
Chemistry, Multidisciplinary
Hiroki Sakuta, Naoki Nakatani, Takayuki Torisawa, Yutaka Sumino, Kanta Tsumoto, Kazuhiro Oiwa, Kenichi Yoshikawa
Summary: Water phase separation in cells can lead to mechanical motion by entrapping protein motors and generating vortex flow inside cell-sized droplets. This study reveals that the water phase separation interface can drive translational motion of droplets by spontaneously entrapping kinesins and microtubules and generating vortex flow. The findings highlight the importance of water phase separation in both chemical and mechanical processes.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Mayu Shono, Fumika Fujita, Kenichi Yoshikawa, Akihisa Shioi
Summary: Stable cell-sized droplets entrapping DNA molecules are generated through micro segregation. Measurements of electrification and Zeta potentials confirmed the presence of negatively charged droplets trapping the DNA.
