Review
Plant Sciences
Nobutoshi Yamaguchi
Summary: This article summarizes the importance of gene regulatory networks in plant reproductive development and discusses the recent advances in utilizing genetic engineering and chemical application to modulate the epigenetic regulation of gene expression.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Computer Science, Information Systems
Anargyros J. Roumeliotis, Christos N. Efrem, Charilaos I. Kourogiorgas, Athanasios D. Panagopoulos
Summary: This article focuses on studying the one-to-many suboptimal assignments in high-throughput multibeam satellite systems under the smart gateway diversity concept. It proposes a two-step heuristic approach to approach the optimal solutions and introduces new metrics for investigation.
IEEE SYSTEMS JOURNAL
(2022)
Review
Cardiac & Cardiovascular Systems
Miron Sopic, Emma L. Robinson, Costanza Emanueli, Prashant Srivastava, Claudio Angione, Carlo Gaetano, Gianluigi Condorelli, Fabio Martelli, Thierry Pedrazzini, Yvan Devaux
Summary: The field of epigenetics has gained attention in cardiovascular research due to its association with disease development. Multi-omics approaches that integrate different levels of disease regulation, such as DNA, histone, and RNA modifications, are essential for understanding complex diseases like cardiovascular diseases. This review focuses on discussing the role of epigenetic mechanisms in regulating gene expression and their interlinkage in the development of cardiac disease, particularly heart failure. The review also presents current methods and tools used for data integration and analysis, which can contribute to the discovery of novel therapeutic approaches and biomarkers for precision healthcare and improved clinical outcomes.
BASIC RESEARCH IN CARDIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
Article
Plant Sciences
Pol Laanen, Ann Cuypers, Eline Saenen, Nele Horemans
Summary: As sessile organisms, plants acclimate or adapt to unfavorable conditions in order to survive. Flower induction regulation is crucial for reproduction and species survival. The effects of ionising radiation on flowering, including gene pathways and epigenetics, need to be studied for environmental radiation protection.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Yijian Zou, Karthik Siva, Tomohiro Soejima, Roger S. K. Mong, Michael P. Zaletel
Summary: This study introduces two related non-negative measures of tripartite entanglement and shows that states with nonzero measures have nontrivial entanglement. Additionally, it demonstrates that these entanglement measures in one dimension depend only on the emergent low-energy theory. For a gapped system, it argues that entanglement measures either both nonzero or both zero, depending on the system's ground state. Furthermore, a numerical algorithm is developed for computing entanglement measures in critical systems.
PHYSICAL REVIEW LETTERS
(2021)
Review
Immunology
Isabella Fraschilla, Hajera Amatullah, Kate L. Jeffrey
Summary: The innate immune system has the ability to rapidly initiate transcriptional programs in response to specific pathogens, depending on dynamic chromatin states. This review discusses the chromatin processes involved in innate immune cell differentiation, functional transcriptional responses, and how they can be maladapted in diseases. Novel therapeutic approaches for cellular reprogramming are also discussed.
CURRENT OPINION IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Stefan Birnkammer, Alvise Bastianello, Michael Knap
Summary: This study investigates the thermalization dynamics after a quantum quench in confined systems and finds that it exhibits multiple stages. Taking the confined Ising spin chain as an example, bound states resembling mesons are formed. The system first reaches a prethermal state related to the number of conserved mesons, and then achieves true thermal equilibrium at much later times.
NATURE COMMUNICATIONS
(2022)
Review
Immunology
Shubham Tripathi, John S. Tsang, Kyemyung Park
Summary: Regulatory T cells have crucial roles in immune homeostasis and response. A systems immunology approach can advance our understanding of Treg function and identify general principles of immune regulation.
TRENDS IN IMMUNOLOGY
(2023)
Review
Plant Sciences
Yukun Wang, Hong Ye, Jianfang Bai, Fei Ren
Summary: Developmentally programmed cell death plays a vital role in regulating floral organ growth and development, involving factors such as tapetal degeneration, pollen tube rupture, receptive synergid cell death, nucellar degradation, and antipodal cell degradation. Understanding the complex molecular networks involved in floral dPCD processes provides insights into flower-specific dPCD process.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Plant Sciences
Saet Buyl Lee, Mi Chung Suh
Summary: This study summarizes the regulatory mechanisms underlying cuticular wax biosynthesis in plants, including transcriptional, post-transcriptional, post-translational, and epigenetic levels. The advances in our understanding of these regulatory mechanisms have improved our knowledge of how plants balance carbon metabolic pathways between optimal growth and development and defense against abiotic stresses.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Mathematical & Computational Biology
Abhijeet Rajendra Sonawane, Dawn L. DeMeo, John Quackenbush, Kimberly Glass
Summary: The study focuses on the application of epigenetic data in gene regulatory networks, developing the SPIDER method for network reconstruction, which shows high accuracy and cell-line-specific interactions, and has the potential to identify novel hypotheses for better characterizing cell-type and phenotype-specific regulatory mechanisms.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Review
Oncology
Amaia Arruabarrena-Aristorena, Eneda Toska
Summary: The majority of breast cancers are ER+, and agents targeting the ER signaling pathway have significantly improved survival for patients. However, therapeutic resistance is a challenge, particularly in metastatic cases. In recent years, disrupted epigenetic regulatory processes have been identified as major contributors to cancer development, including breast cancer. Aberrations in chromatin modifiers and transcription factors have also been associated with breast cancer development and treatment outcomes, leading to the proposal of new epigenetic-based therapies in combination with targeted treatments to overcome resistance.
FRONTIERS IN ONCOLOGY
(2022)
Review
Plant Sciences
Yunzhuan Zhou, Fuxiang Xu, Yanan Shao, Junna He
Summary: As global warming intensifies, the earth's average temperature continues to rise. Plants have developed two main mechanisms, the heat stress response and the thermomorphogenesis response, to cope with elevated temperatures. This review summarizes recent progress in understanding these heat-responsive molecular regulatory pathways in plants and discusses future perspectives in this field.
Review
Immunology
Tom Sidwell, Ellen V. Rothenberg
Summary: Bcl11b, a critical transcription factor, plays context-dependent roles in the development of different cell types. Its chromatin binding activity is largely guided by interactions with other transcription factors, and it recruits multiple families of chromatin-modifying enzyme complexes to induce changes in regional suites of epigenetic modifications.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Nobutoshi Yamaguchi, Satoshi Matsubara, Kaori Yoshimizu, Motohide Seki, Kouta Hamada, Mari Kamitani, Yuko Kurita, Yasuyuki Nomura, Kota Nagashima, Soichi Inagaki, Takamasa Suzuki, Eng-Seng Gan, Taiko To, Tetsuji Kakutani, Atsushi J. Nagano, Akiko Satake, Toshiro Ito
Summary: Acclimation to high temperature increases plants' tolerance of subsequent lethal high temperatures. The study reveals that JUMONJI H3K27me3 demethylases are essential for heat acclimation in Arabidopsis. This epigenetic memory mechanism involving histone demethylases could have significant implications for environmental adaptation of field plants.
NATURE COMMUNICATIONS
(2021)
Review
Plant Sciences
Nobutoshi Yamaguchi
Summary: H3K27me3 modification is a conserved epigenetic signal for transcriptional repression in plants and animals, with JMJ genes regulating the demethylation of H3K27 in Arabidopsis thaliana. Transcription of JMJ genes plays a crucial role in plant development and environmental responses, working synergistically with transcription factors and other epigenetic regulators.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Nobutoshi Yamaguchi
Summary: Certain eukaryotic transcription factors have the ability to reprogram one cell type into another, with pioneer factors being able to engage target sites in closed chromatin. In plants, the TF LEAFY acts as a pioneer factor specifying floral fate and interacts with other factors to regulate floral development.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Nobutoshi Yamaguchi
Summary: This article summarizes the importance of gene regulatory networks in plant reproductive development and discusses the recent advances in utilizing genetic engineering and chemical application to modulate the epigenetic regulation of gene expression.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Editorial Material
Plant Sciences
Nobutoshi Yamaguchi
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Alfino Sebastian, Ilham Cahyo Nugroho, Herdin Surya Dwi Putra, Febri Adi Susanto, Putri Wijayanti, Nobutoshi Yamaguchi, Tri Rini Nuringtyas, Yekti Asih Purwestri
Summary: This study investigated the diversity of drought mitigation strategies and the related genes in pigmented rice varieties. It was found that Merah Pari Eja showed the highest drought tolerance among the cultivars, which was supported by gene expression profiling and measurements of antioxidant enzyme activity and leaf damage.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2022)
Article
Plant Sciences
Anik Hidayah, Rizka Rohmatin Nisak, Febri Adi Susanto, Tri Rini Nuringtyas, Nobutoshi Yamaguchi, Yekti Asih Purwestri
Summary: Seed halopriming treatment can improve salinity tolerance in susceptible and moderately tolerant rice cultivars.
Article
Biochemistry & Molecular Biology
Margaret Anne Pelayo, Fumi Morishita, Haruka Sawada, Kasumi Matsushita, Hideaki Iimura, Zemiao He, Liang Sheng Looi, Naoya Katagiri, Asumi Nagamori, Takamasa Suzuki, Marek Sirl, Ales Soukup, Akiko Satake, Toshiro Ito, Nobutoshi Yamaguchi
Summary: Cell cycle-coupled H3K27me3 dilution regulates floral development by controlling the expression timing of various target genes. The transcription factor AG prevents maintenance of H3K27me3 along the KNU coding sequence, allowing activation of KNU transcription prior to floral meristem termination. AHL18, a downstream target of AG, is specifically expressed in stamens and involved in stamen growth. Our findings highlight the importance of cell cycle-coupled H3K27me3 dilution in floral development and provide insights into the regulatory mechanisms.
Review
Biochemistry & Molecular Biology
Xuejing Wang, Nicholas Wui Kiat Tan, Fong Yi Chung, Nobutoshi Yamaguchi, Eng-Seng Gan, Toshiro Ito
Summary: Heat stress is a growing threat to food security due to global warming. Plants, as sessile species, have developed different mechanisms to cope with the disruption of cellular homeostasis caused by heat stress. This article summarizes the transcriptional regulation mechanisms mediated by transcription factors, epigenetic regulators, and regulatory RNAs in response to heat stress. Additionally, cellular activities such as protein homeostasis maintenance and regulation of ROS homeostasis are discussed. The harmonious regulation of plant cells allows them to adapt to unfavorable environments. Future studies on improving crop resilience to heat stress for urban agriculture are also suggested.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Yekti Asih Purwestri, Siti Nurbaiti, Sekar Pelangi Manik Putri, Ignasia Margi Wahyuni, Siti Roswiyah Yulyani, Alfino Sebastian, Tri Rini Nuringtyas, Nobutoshi Yamaguchi
Summary: Unfavorable environmental conditions and climate change can cause yield losses in plants. Indonesian pigmented rice cultivars with high anthocyanin contents have great potential for cultivation, but their ability to grow in high-salinity lands is limited. In this study, we examined the effect of pre-treating the seeds with a halopriming solution on salt tolerance. Halopriming alleviated the negative effects of salinity on plant growth by reducing reactive oxygen species accumulation and increasing the stability of the membrane and photosynthetic pigment contents. The effects of halopriming on proline accumulation and stress-related gene expression varied among rice varieties.
Article
Plant Sciences
Sota Fujii, Eri Yamamoto, Seitaro Ito, Surachat Tangpranomkorn, Yuka Kimura, Hiroki Miura, Nobutoshi Yamaguchi, Yoshinobu Kato, Maki Niidome, Aya Yoshida, Hiroko Shimosato-Asano, Yuko Wada, Toshiro Ito, Seiji Takayama
Summary: Pre-zygotic interspecies incompatibility is an important defense mechanism in plants to prevent interspecies pollen transfers. This study identifies SPRI2/SRS7, a transcription factor, as a key regulator of interspecies reproductive barriers in Arabidopsis. SPRI2/SRS7 regulates the transcripti could contribute to the establishment of interspecific reproductive barriers.
Article
Biochemistry & Molecular Biology
Nobutoshi Yamaguchi, Toshiro Ito
Summary: This study computationally characterized the expression patterns of JMJ H3K27me3 demethylase genes using public transcriptome datasets, revealing JMJ30 to be highly expressed in the L1 layer of Arabidopsis shoot apical meristem and most affected by abiotic and biotic stress. The expression of JMJ30 varied among Arabidopsis thaliana accessions, suggesting that transcriptional changes of H3K27me3 demethylase genes may play key roles in development and environmental responses. Additionally, the expression of a JMJ30 orthologue from Arabidopsis halleri fluctuated under field conditions, further supporting the importance of these genes in plant adaptation.
PLANT SIGNALING & BEHAVIOR
(2021)
