Review
Virology
Stephen P. Goff
Summary: This review provides an overview of the silencing mechanisms of retroviral DNA, discussing its impact on virus replication, the sensing of the virus by the innate immune system, and the formation of latent proviruses. Additionally, it speculates on the potential transition to high expression from integrated proviruses in permissive cell types, as well as the silencing of proviruses even after integration in embryonic stem cells and other developmentally primitive cell types.
Article
Plant Sciences
Patrick Ferreira, Abdessalem Chahed, Leticia M. Estevinho, Natalia Seixas, Rodrigo Costa, Altino Choupina
Summary: Ink disease is a significant cause of decline in chestnut orchards, with the Phytophthora cinnamomi being the main pathogen responsible for the disease in Portugal. This highly aggressive and widely distributed plant pathogen causes economic losses and decline in numerous plant species. Effective treatments are currently unavailable.
Article
Multidisciplinary Sciences
Bo Zhang, Chen Zhao, Wenchen Shen, Wei Li, Yue Zheng, Xiangfei Kong, Junbao Wang, Xudong Wu, Tao Zeng, Ying Liu, Yan Zhou
Summary: The hippocampus plays a crucial role in learning and memory, and its development requires precise coordination of cell patterning, proliferation, differentiation, and migration. In this study, it was found that KDM2B mediates a gene repressive program that controls fate specification and cell migration in the hippocampus, affecting its morphology and related behaviors.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Marlies Wouters, Heloise Bastiaanse, Stephane Rombauts, Lisanne de Vries, Tim De Pooter, Mojca Strazisar, Godfrey Neutelings, Ruben Vanholme, Wout Boerjan
Summary: The dwarfed phenotype of the Arabidopsis cinnamoyl-CoA reductase 1-6 intronic transfer DNA (T-DNA) lignin mutant is restored by the introduction of additional T-DNAs sharing identical sequences.
Article
Cell Biology
Nadezda A. Fursova, Anne H. Turberfield, Neil P. Blackledge, Emma L. Findlater, Anna Lastuvkova, Miles K. Huseyin, Paula Dobrinic, Robert J. Klose
Summary: Histone modifications play crucial roles in gene regulation and development, with little known about modifications found broadly throughout the genome. BAP1 deubiquitylase constrains H2AK119ub1 accumulation throughout the genome, impacting gene expression and transcription. Failure to constrain H2AK119ub1 compromises Polycomb complex occupancy at certain target genes, resulting in their derepression.
GENES & DEVELOPMENT
(2021)
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
Biochemistry & Molecular Biology
Liangbing Yuan, Xin Song, Lu Zhang, Yaoguang Yu, Zhenwei Liang, Yawen Lei, Jiuxiao Ruan, Bin Tan, Jun Liu, Chenlong Li
Summary: The study reveals that the transcriptional repressors VAL1 and VAL2 recruit PRC2 to target loci in Arabidopsis thaliana. They physically interact with PRC2 catalytic subunits SWN and CLF, colocalize at target loci, and regulate H3K27me3 levels, affecting transcription.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Zhen Wang, Junmei Kang, Juan Armando Casas-Mollano, Yongchao Dou, Shangang Jia, Qingchuan Yang, Chi Zhang, Heriberto Cerutti
Summary: The plant-specific protein kinase MLK4 regulates flowering time by phosphorylating histone H3, which in turn accelerates flowering by repressing the transcription of the negative flowering regulator FLC/MAF.
Article
Biochemistry & Molecular Biology
Dong Cheng, Zhaoming Dong, Ping Lin, Guanwang Shen, Qingyou Xia
Summary: This study reveals the crucial role of acetylation modification and chromatin accessibility in the transcriptional activation of ecdysone-responsive genes during insect development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Ruijie Cai, Runyu Lv, Xin'e Shi, Gongshe Yang, Jianjun Jin
Summary: CRISPR/Cas9-mediated gene editing has been widely used due to its programmability and specificity, but can also affect genome stability. Recently, fusion proteins with transcriptional activator/inhibitor effects have been developed by linking proteins to dCas9 to regulate gene transcription. These tools have important applications in gene regulation, functional studies, target gene screening, and disease treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Helene Dubois-Pot-Schneider, Caroline Aninat, Kathrin Kattler, Karim Fekir, Kathleen Jarnouen, Virginie Cerec, Denise Glaise, Abdulrahman Salhab, Gilles Gasparoni, Kubo Takashi, Seiichi Ishida, Joern Walter, Anne Corlu
Summary: DMSO influences liver-specific gene expression and regulates gene expression through multiple regulatory factors, as well as histone acetylation and deacetylation. Additionally, there is an interplay between cytoskeleton organization and extracellular matrix remodeling with hepatocyte maturation.
Article
Biochemistry & Molecular Biology
Fengling Lai, Yibin Cheng, Juan Zou, Haoyu Wang, Wang Zhu, Xin Wang, Hanhua Cheng, Rongjia Zhou
Summary: This study examined histone modifications in gonadal differentiation, identifying new modification sites and their relationship with different types of gonadal differentiation. The research also discovered a testis-enriched histone modification site associated with spermatogenesis, emphasizing the importance of histone modifications in the transcriptional regulation of sex-determining genes during gonadal development.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Nicolas Butel, Agnes Yu, Ivan Le Masson, Filipe Borges, Taline Elmayan, Christelle Taochy, Nial R. Gursanscky, Jiangling Cao, Shengnan Bi, Anne Sawyer, Bernard J. Carroll, Herve Vaucheret
Summary: The research reveals that there are discrepancies in the epigenetic behavior of transgenes and endogenous genes in Arabidopsis, indicating that they are regulated by different mechanisms.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Thomas Dahlet, Matthias Truss, Ute Frede, Hala Al Adhami, Anais F. Bardet, Michael Dumas, Judith Vallet, Johana Chicher, Philippe Hammann, Sarah Kottnik, Peter Hansen, Uschi Luz, Gonzalo Alvarez, Ghislain Auclair, Jochen Hecht, Peter N. Robinson, Christian Hagemeier, Michael Weber
Summary: During mouse development, the transcription factor E2F6 is crucial in targeting CpG island DNA methylation and epigenetic silencing to germline genes, especially in early embryonic cells. The cooperation between E2F6 and MGA is essential for silencing a subgroup of germline genes, dependent on the E2F6 marked box domain. E2F6 is required for initiating epigenetic silencing in early embryonic cells but becomes dispensable for maintenance in differentiated cells.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Zichong Li, Steven G. Deeks, Melanie Ott, Warner C. Greene
Summary: In this study, a method called REACTS was developed to explore the synergies between HIV transcription repressors. Multiple synergies between host repressors were identified, providing a potential target for overcoming HIV rebound after ART cessation.
Article
Biotechnology & Applied Microbiology
Fantao Kong, Tomohito Yamasaki, Sari Dewi Kurniasih, Liyuan Hou, Xiaobo Li, Nina Ivanova, Shigeru Okada, Takeshi Ohama
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2015)
Article
Plant Sciences
Tomohito Yamasaki, Eun-Jeong Kim, Heriberto Cerutti, Takeshi Ohama
Article
Biochemistry & Molecular Biology
Sari Dewi Kurniasih, Tomohito Yamasaki, Fantao Kong, Sigeru Okada, Dwiyantari Widyaningrum, Takeshi Ohama
PLANT MOLECULAR BIOLOGY
(2016)
Article
Multidisciplinary Sciences
Tomohito Yamasaki, Masayuki Onishi, Eun-Jeong Kim, Heriberto Cerutti, Takeshi Ohama
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biotechnology & Applied Microbiology
Fantao Kong, Tomohito Yamasaki, Takeshi Ohama
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2014)
Article
Multidisciplinary Sciences
Adam Voshall, Eun-Jeong Kim, Xinrong Ma, Tomohito Yamasaki, Etsuko N. Moriyama, Heriberto Cerutti
SCIENTIFIC REPORTS
(2017)
Article
Biotechnology & Applied Microbiology
Masanori Hiraoka, Kouki Tanaka, Tomohito Yamasaki, Osamu Miura
JOURNAL OF APPLIED PHYCOLOGY
(2020)
Article
Multidisciplinary Sciences
Ryutaro Tokutsu, Konomi Fujimura-Kamada, Takuya Matsuo, Tomohito Yamasaki, Jun Minagawa
NATURE COMMUNICATIONS
(2019)
Article
Cell Biology
Yutaro Kinoshita, Yoichi Sato, Tetsuya Sakurai, Tomohito Yamasaki, Hirofumi Yamamoto, Masanori Hiraoka
Summary: The mechanism of cellular differentiation and multicellular morphogenesis in multicellular marine algae remains mostly unknown. A study on the leafy seaweed Gayralia oxysperma revealed that its blade cells maintain their totipotency, while its rhizoid cells lose the ability to divide and differentiate. This is in contrast to the previously studied Ulva, suggesting that the morphogenesis system in Gayralia is fundamentally different and requires further investigation.
Article
Biotechnology & Applied Microbiology
Ayat J. S. Al-Azab, Yuichi Aoki, Fean D. Sarian, Yuki Sori, Dwiyantari Widyaningrum, Tomohito Yamasaki, Fantao Kong, Takeshi Ohama
Summary: Exposure to resin nanoparticles composed of isobutyl cyanoacrylate polymers can induce acute cell death in microalgal species. The upregulation of genes encoding antioxidant enzymes and cell wall hydrolytic enzymes plays a key role in inducing cell death in Chlamydomonas reinhardtii.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Multidisciplinary Sciences
Tomohito Yamasaki, Ryutaro Tokutsu, Haruhi Sawa, Nazifa Naziha Razali, Momoka Hayashi, Jun Minagawa
Summary: Small RNAs form complexes with Argonaute proteins to repress gene expression. In the green alga Chlamydomonas reinhardtii, sRNAs contribute to the induction of photoprotection mediated by the blue-light receptor phototropin (PHOT) and the expression of LIGHT HARVESTING COMPLEX STRESS-RELATED 3 (LHCSR3). The sRNAs regulate the degree of photoprotection by controlling the expression of PHOT.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Xiaowei Pan, Ryutaro Tokutsu, Anjie Li, Kenji Takizawa, Chihong Song, Kazuyoshi Murata, Tomohito Yamasaki, Zhenfeng Liu, Jun Minagawa, Mei Li
Summary: The study provides high-resolution structures of the PSI-LHCI-LHCII supercomplex from Chlamydomonas reinhardtii, elucidating the assembly mechanism between the PSI-LHCI complex and phosphorylated LHCII trimers, as well as the direct interactions between specific LhcbM isoforms and the PSI core. Functional studies on mutant strains lacking LhcbM1 or LhcbM5 demonstrate that only LhcbM5 is essential for supercomplex formation, revealing specific interactions and potential energy transfer pathways between green algal PSI and phosphorylated LHCIIs.
Article
Plant Sciences
Ryutaro Tokutsu, Konomi Fujimura-Kamada, Tomohito Yamasaki, Keisuke Okajima, Jun Minagawa
Summary: Photosynthesis in chloroplasts is crucial for photoautotrophic growth, while non-photochemical quenching (NPQ) helps prevent the generation of reactive oxygen species under excess light. In the green alga Chlamydomonas reinhardtii, UV light activates NPQ-dependent photoprotection more rapidly than visible light, leading to faster gene expression and protein accumulation related to photoprotection. The action spectrum of UV-dependent induction of photoprotective factors suggests that C. reinhardtii senses longer-wavelength UV compared to the dicot plant Arabidopsis, indicating a unique UV response in green algae.
Article
Multidisciplinary Sciences
Ryutaro Tokutsu, Konomi Fujimura-Kamada, Tomohito Yamasaki, Takuya Matsuo, Jun Minagawa
SCIENTIFIC REPORTS
(2019)
Article
Plant Sciences
Yusuke Aihara, Konomi Fujimura-Kamada, Tomohito Yamasaki, Jun Minagawa