Review
Plant Sciences
Huijia Kang, Tianyi Fan, Jiabing Wu, Yan Zhu, Wen-Hui Shen
Summary: Plants, as sessile organisms, are constantly exposed to diverse stresses, including pathogen invasion. Recent studies have found that pathogen infections can induce epigenetic changes in plants, leading to the reprogramming of plant defense genes. These mechanisms could be used in the design of stress-resistant plant varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ann K. Hogan, Kizhakke M. Sathyan, Alexander B. Willis, Sakshi Khurana, Shashank Srivastava, Ewelina Zasadzinska, Alexander S. Lee, Aaron O. Bailey, Matthew N. Gaynes, Jiehuan Huang, Justin Bodner, Celeste D. Rosencrance, Kelvin A. Wong, Marc A. Morgan, Kyle P. Eagen, Ali Shilatifard, Daniel R. Foltz
Summary: Histone chaperones, such as UBR7, play a crucial role in regulating the stability and supply of post-nucleosomal histone complexes. UBR7 interacts with NASP and histones to promote reincorporation of post-nucleosomal H3 complexes, opposing the histone storage functions of NASP. The absence of UBR7 leads to accumulation of NASP-bound post-nucleosomal histones and depletion of H3K4me3-modified histones in chromatin.
Article
Biology
Christine Schleif, Rachel Gewiss, Michael Griswold
Summary: Spermatogonial differentiation is regulated by retinoic acid and involves significant morphological and transcriptional changes. This study aimed to investigate the timing and dynamics of chromatin organization during spermatogonial development and its relationship with transcriptional changes. By using ATAC-seq, the researchers found that 50% of accessible regions in undifferentiated spermatogonia were condensed within 18 hours of retinoic acid action. Surprisingly, genes relevant to spermatogonial development remained accessible at all times, indicating that chromatin state does not directly impact transcription.
Editorial Material
Biology
J. Christian Althaus, Michael A. Sutton
Summary: All-trans retinoic acid induces synaptic plasticity in human cortical circuits by engaging the spine apparatus, leading to structural and functional changes at synapses.
Review
Biochemical Research Methods
Elias Orouji, Ayush T. Raman
Summary: The human genome is shaped by a variety of histone modifications, which play a crucial role in determining chromatin states and organization. Using statistical models and computational tools, noncoding regions of DNA can be annotated and combinatorial histone marks inferred. These marks enable the discovery of genomic function and activity, and their patterns change in different cell conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Plant Sciences
Xiali Ding, Xuhui Jia, Yong Xiang, Wenhui Jiang
Summary: Seeds play a crucial role in plant reproduction and dispersal, undergoing a life cycle from seed development to seedling establishment regulated by physiological and biochemical mechanisms. Recent research has focused intensively on the role of epigenetics in seed behavior, particularly in model plants like rice and Arabidopsis. Emphasis is placed on the impact of epigenetics on tissue formation, gene expression, and environmental responses during the seed life cycle.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Alonso Javier Pardal, Andrew James Bowman
Summary: This study identified importin-5 as the major importin associated with cytoplasmic H3, which transfers its monomeric cargo to nuclear sNASP. Additionally, monomeric H4 interacts specifically with HAT1 and RBBP7. It was found that Imp5 and sNASP compete for binding H3, suggesting a direct interaction site competition requiring GTP-bound Ran for histone transfer.
Article
Plant Sciences
Jiabing Wu, Yue Yang, Jiachen Wang, Youchao Wang, Liufan Yin, Zengxuan An, Kangxi Du, Yan Zhu, Ji Qi, Wen-Hui Shen, Aiwu Dong
Summary: In Arabidopsis, AtChz1A and AtChz1B are histone chaperones that bind to H2A.Z-H2B and facilitate nucleosome assembly. They interact with SWR1 subunit ARP6 and play critical roles in the deposition of H2A.Z, thereby regulating the transcription of genes involved in flowering and other processes.
Review
Biochemistry & Molecular Biology
Ann K. Hogan, Daniel R. Foltz
Summary: The eukayrotic genome is packaged into chromatin, with nucleosomes being the basic unit composed of DNA and histones. Histones, stable protein species in mammalian cells, play a crucial role in homeostasis. While histones are generally stable, their degradation is necessary in specific conditions for organismal and cellular fitness.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu, Jizeng Jia
Summary: In this study, the association between transposons (TEs), chromatin states, and chromatin accessibility in Aegilops tauschii was analyzed. It was found that TEs contributed to the diverse distribution of chromatin states and affected the chromatin state and openness of potential regulatory elements. Some TE superfamilies carried active/open chromatin regions. Furthermore, the accessibility shaped by TEs was associated with the histone mark H3K9ac. These findings highlight the role of TEs in shaping the epigenetic landscape and regulating gene expression in Aegilops tauschii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Shuai Zhao, Kelly N. Chuh, Baichao Zhang, Barbara E. Dul, Robert E. Thompson, Lorna A. Farrelly, Xiaohui Liu, Ning Xu, Yi Xue, Robert G. Roeder, Ian Maze, Tom W. Muir, Haitao Li
Summary: The study found that the readers of H3K4me3 retain binding to H3K4me3Q5ser, while the erasers are significantly inhibited. The results suggest that H3Q5ser may potentially fine-tune critical gene expression programs by stabilizing H3K4me3 from dynamic turnover or enhancing its physical readout by downstream effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Rocio Nunez-Vazquez, Benedicte Desvoyes, Crisanto Gutierrez
Summary: Plants have developed various mechanisms to adapt to abiotic stresses, which involve transcriptional regulation and chromatin modifications. Understanding and manipulating these regulatory networks are crucial for enhancing crop resilience and performance against stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Adrian Arrieta, Thomas M. Vondriska
Summary: Maintenance of protein folding homeostasis is crucial for cell survival and cell-specific biological processes. Chromatin organization plays a vital role in cell type specification. Nucleosome organization and histone turnover are key factors in chromatin organization. This review focuses on the criticality of nucleosome proteostasis, the involvement of histone chaperones and ATP-dependent chromatin remodelers, and the disrupted nucleosome proteostasis mechanisms in diseases.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Cell Biology
Peijun Wang, Wanting Yang, Shuxin Zhao, Buhe Nashun
Summary: This article discusses the important role of the histone chaperone facilitates chromatin transcription (FACT) in the cell cycle, analyzing its structural characteristics and functions. It explores how FACT regulates chromatin reorganization and its potential roles in transcription, replication, DNA repair, and even cell fate determination.
Article
Cell Biology
Liying Wang, Zhiliang Xu, Libin Wang, Chao Liu, Huafang Wei, Ruidan Zhang, Yinghong Chen, Lina Wang, Wenwen Liu, Sai Xiao, Wei Li, Wei Li
Summary: The study reveals that RNF20 is crucial for early stage somatic cell reprogramming, with Rnf20 knockout leading to failure in reprogramming at the initial stage. The absence of RNF20 affects the transcription of MET-related genes and early pluripotency genes, ultimately hindering the establishment of a pluripotent gene network.
CELL PROLIFERATION
(2021)
Article
Biology
Yuto Sakane, Midori Iida, Takashi Hasebe, Satoshi Fujii, Daniel R. Buchholz, Atsuko Ishizuya-Oka, Takashi Yamamoto, Ken-ichi T. Suzuki
Article
Genetics & Heredity
Masatoshi Matsunami, Miyuki Suzuki, Yoshikazu Haramoto, Akimasa Fukui, Takeshi Inoue, Katsushi Yamaguchi, Ikuo Uchiyama, Kazuki Mori, Kosuke Tashiro, Yuzuru Ito, Takashi Takeuchi, Ken-ichi T. Suzuki, Kiyokazu Agata, Shuji Shigenobu, Toshinori Hayashi
Article
Biochemistry & Molecular Biology
Takeshi Ikeda, Kohei Ichikawa, Hajime Shigeto, Takenori Ishida, Ryuichi Hirota, Hisakage Funabashi, Akio Kuroda
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2019)
Article
Environmental Sciences
Yuka Yoshinouchi, Sachiko Shimizu, Jin-Seon Lee, Masashi Hirano, Ken-ichi T. Suzuki, Eun-Young Kim, Hisato Iwata
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2019)
Article
Cell Biology
Midori Iida, Miyuki Suzuki, Yuto Sakane, Hiroyo Nishide, Ikuo Uchiyama, Takashi Yamamoto, Ken-ichi T. Suzuki, Satoshi Fujii
Article
Biotechnology & Applied Microbiology
Gamal Nasser Abdel-Hady, Takeshi Ikeda, Takenori Ishida, Hisakage Funabashi, Akio Kuroda, Ryuichi Hirota
Summary: In this study, a thermotolerant phosphite dehydrogenase from Ralstonia sp. 4506 (RsPtxD) was engineered to create a highly efficient and robust NADPH regeneration system. By changing specific amino acid residues, a mutant RsPtxD(HARRA) with significantly increased preference for NADP was obtained, displaying the highest catalytic efficiency among previously reported phosphite dehydrogenases. This mutant exhibited high thermostability and organic solvent tolerance, making it a promising alternative NADPH regeneration system for practical applications.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Correction
Biochemical Research Methods
Kei Motomura, Kosuke Sano, Satoru Watanabe, Akihiro Kanbara, Gamal Nasser Abdel-Hady, Takeshi Ikeda, Takenori Ishida, Hisakage Funabashi, Akio Kuroda, Ryuichi Hirota
ACS SYNTHETIC BIOLOGY
(2021)
Article
Plant Sciences
Narumi Toda, Hiroki Murakami, Akihiro Kanbara, Akio Kuroda, Ryuichi Hirota
Summary: The study on using phosphite (Pt) to suppress predatory zooplankton Poterioochromonas malhamensis showed that high concentrations of Pt reduced the grazing impact of P. malhamensis. Furthermore, the suppression effect of Pt was found to be dependent on the type of environmental water used, and under high Pt conditions, Paraphysomonas emerged as a dominant microorganism replacing P. malhamensis.
Article
Instruments & Instrumentation
Hisakage Funabashi, Keisuke Nakatsuka, Shuhei Yoshida, Hajime Shigeto, Ryuichi Hirota, Takeshi Ikeda, Akio Kuroda
Summary: The design and feasibility of split G-quadruplex-based DNA nanotweezers that can detect short nucleic acids with a single-base mismatch are discussed. These nanotweezers exhibit peroxidase activity and can be used for homogeneous assay format to detect specific nucleic acids. Additionally, a new type of DNA-BNA chimera nanotweezers has been developed, which can distinguish different miRNA sequences based on the difference in melting temperature.
SENSORS AND MATERIALS
(2022)
Article
Biochemical Research Methods
Ryuichi Hirota, Zen-ichiro Katsuura, Naoki Momokawa, Hiroki Murakami, Satoru Watanabe, Takenori Ishida, Takeshi Ikeda, Hisakage Funabashi, Akio Kuroda
Summary: In this study, it was found that under specific conditions, a phosphite-dependent strain of Escherichia coli can generate escape mutants. The mutation occurs at position 210 of the transmembrane domain protein HtxC of the phosphorus compound transporter HtxBCDE. The replacement of a specific amino acid residue at this position can reduce the rate of escape mutant generation.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Hiroki Murakami, Kosuke Sano, Kei Motomura, Akio Kuroda, Ryuichi Hirota
Summary: Biological containment is a biosafety strategy used to prevent the spread of genetically modified organisms in natural ecosystems. A study assessed the risk of horizontal gene transfer (HGT) mediated escape in a phosphite-dependent cyanobacterium. The results showed that HGT from closely related species posed a high risk for escape, and inhibiting exogenous DNA uptake could enhance the robustness of the containment system.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2023)
Article
Microbiology
Luke Bown, Ryuichi Hirota, Michelle N. Goettge, Jerry Cui, David T. Krist, Lingyang Zhu, Constantin Giurgiu, Wilfred A. van der Donk, Kou-San Ju, William W. Metcalf
Summary: The study reveals the biosynthetic pathway of phosphonothrixin, which can help design strains that overproduce this potentially useful herbicide.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Multidisciplinary Sciences
Takenori Ishida, Takuma Hashimoto, Kanako Masaki, Hisakage Funabashi, Ryuichi Hirota, Takeshi Ikeda, Hideji Tajima, Akio Kuroda
SCIENTIFIC REPORTS
(2020)
Article
Chemistry, Analytical
Hajime Shigeto, Takuto Ono, Takeshi Ikeda, Ryuichi Hirota, Takenori Ishida, Akio Kuroda, Hisakage Funabashi
Article
Genetics & Heredity
Takenori Ishida, Nobutoshi Fujihara, Tomoki Nishimura, Hisakage Funabashi, Ryuichi Hirota, Takeshi Ikeda, Akio Kuroda
GENES AND ENVIRONMENT
(2019)