Review
Cell Biology
A. K. Balaji, Santam Saha, Shruti Deshpande, Darshini Poola, Kundan Sengupta
Summary: Dysregulation of chromatin remodeling and nuclear envelope proteins plays a significant role in cancer development. Recent advances in single-cell sequencing, imaging technologies, and data mining approaches enable the design of small molecules to selectively inhibit cancer cell growth and proliferation in a genome- and epigenome-specific manner.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Norma E. Padilla-Mejia, Ludek Koreny, Jennifer Holden, Marie Vancova, Julius Lukes, Martin Zoltner, Mark C. Field
Summary: The nuclear lamina plays crucial roles in maintaining nuclear structure and controlling gene expression. In trypanosomes, the N- and C-termini of NUP-1 act as interaction hubs and impact other components of the lamina and nuclear envelope.
JOURNAL OF CELL SCIENCE
(2021)
Article
Cell Biology
Isabelle Loiodice, Mickael Garnier, Ivaylo Nikolov, Angela Taddei
Summary: Silent chromatin in eukaryotic cells is mainly located at the nuclear periphery, and the establishment of silencing is a stepwise process occurring over several cell cycles. Studying a budding yeast model, researchers have identified mechanisms and protein recruitment relationships during the process of establishing silencing at an ectopic locus.
Article
Biochemical Research Methods
Sarah M. Mangiameli, Haiqi Chen, Andrew S. Earl, Julie A. Dobkin, Daniel Lesman, Jason D. Buenrostro, Fei Chen
Summary: Photoselective sequencing is a new method for genomic and epigenomic profiling in morphologically distinct regions. It uses targeted illumination to selectively unblock a photocaged fragment library, enabling sequencing-based readout in microscopically identified spatial regions. The method was validated by analyzing chromatin accessibility profiles of fluorescently-labeled cell types in the mouse brain and comparing with published data. Photoselective sequencing is a flexible and generalizable platform for studying the interplay of spatial structures with genomic and epigenomic properties.
Article
Multidisciplinary Sciences
Cheryl L. Smith, Yemin Lan, Rajan Jain, Jonathan A. Epstein, Andrey Poleshko
Summary: The nuclear architecture of rod photoreceptor cells in nocturnal mammals differs from that of other animal cells, with euchromatin and heterochromatin occupying opposite positions. This unique structure is achieved through global relabeling of the rod cell epigenome, involving histone modifications such as H3K9 methylation. This study highlights the significance of epigenetic changes in shaping nuclear architecture in postmitotic cells.
Review
Biochemistry & Molecular Biology
Irina Bogolyubova, Dmitry Bogolyubov
Summary: DAXX is a multifunctional protein involved in various cellular processes, interacting with transcription factors and chromatin-remodeling proteins in the nucleus. Its specific function in mammalian early development as a chaperone of H3.3 supports proper development, impacting recruitment of ATRX and transcription of tandem repeats. Loss of DAXX results in decreased viability of early embryos.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Qin Peng, Ziliang Huang, Kun Sun, Yahan Liu, Chi Woo Yoon, Reed E. S. Harrison, Danielle L. Schmitt, Linshan Zhu, Yiqian Wu, Ipek Tasan, Huimin Zhao, Jin Zhang, Sheng Zhong, Shu Chien, Yingxiao Wang
Summary: Genome architecture and organization are crucial for cell life, but how they coordinate gene expression and determine cell fate at the single cell level remains unknown. The researchers developed a system called SIMBA which allows for simultaneous imaging and manipulation of genomic loci using biomolecular assemblies. This system can enhance imaging signals and recruit epigenetic modulators to repress transcription at specific genomic loci, making it a valuable tool for visualizing and manipulating gene expression in living cells.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Myron Barber Child, Jack R. Bateman, Amir Jahangiri, Armando Reimer, Nicholas C. Lammers, Nica Sabouni, Diego Villamarin, Grace C. McKenzie-Smith, Justine E. Johnson, Daniel Jost, Hernan G. Garcia
Summary: Research suggests that somatic homolog pairing in fruit fly may be driven by specifically interacting 'buttons' encoded along chromosomes, and a quantitative biophysical model has been proposed to demonstrate this hypothesis.
Article
Cell Biology
Koh Nakayama, Sigal Shachar, Elizabeth H. Finn, Hiroyuki Sato, Akihiro Hirakawa, Tom Misteli
Summary: Chromosome structure and nuclear organization play important roles in gene expression regulation. The relationship between the 3D position of a gene in the nucleus and its activity is still not clear. A study on nearly 100 hypoxia-responsive genes found that most of them are located in the intermediate region of the nucleus, and some of them change their position under hypoxic conditions. However, gene position changes are not directly related to gene activity.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Biology
Anna E. Mammel, Heather Z. Huang, Amanda L. Gunn, Emma Choo, Emily M. Hatch
Summary: The length and gene density of the trapped chromosome are key factors determining the membrane stability and timing of rupture of micronuclei. Nuclear envelope composition defects only partly explain the membrane stability in micronuclei.
LIFE SCIENCE ALLIANCE
(2022)
Article
Polymer Science
Mehdi Ravandeh, Masoud Mehrjoo, Konstantin Kharitonov, Jan Schaefer, Antje Quade, Bruno Honnorat, Mabel Ruiz-Lopez, Barbara Keitel, Svea Kreis, Rui Pan, Seung-gi Gang, Kristian Wende, Elke Ploenjes
Summary: Polyethylene terephthalate (PET) is a widely used thermoplastic polyester in industry. Surface modification is required for printing and coating processes, and plasma treatment is commonly used to increase the hydrophilicity of PET films. This study used X-ray ptychography and scanning electron microscopy to investigate the effects of plasma treatment on the surface morphology of PET films. The results showed increased roughness and changes in morphology, as well as an increase in oxygen content and polarity without significant damage to the polymer.
Article
Multidisciplinary Sciences
Meng Zhang, Mary Elisabeth Ehmann, Srija Matukumalli, Aashutosh Girish Boob, David M. Gilbert, Huimin Zhao
Summary: Chromatin boundary elements are difficult to define and characterize. Here the authors report Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains (SHIELD) for high-throughput screening of barrier-type DNA elements in human cells.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Nadav Scher, Katya Rechav, Perrine Paul-Gilloteaux, Ori Avinoam
Summary: By using fluorescently labeled lipid droplets as in situ fiducial markers, correlations between cryo-FM and FIB-SEM datasets can be achieved. Cryo-FIB-SEM imaging provides informative insights into questions related to organelle structure, nuclear organization, and mineral deposits in cells.
Review
Biochemistry & Molecular Biology
Rabia Laghmach, Michele Di Pierro, Davit Potoyan
Summary: The organization and dynamics of chromatin compartments in the cell nucleus are crucial for gene regulation. Recent studies have revealed the dynamic and stochastic nature of chromatin compartments, which may be explained by the phase separation of proteins and nucleic acids. Computational models play a crucial role in understanding the complex interplay of forces that contribute to chromatin dynamics and organization.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Cell Biology
Stefano Giustino Manzo, Lise Dauban, Bas van Steensel
Summary: This article reviews recent advances in the study of LAD-NL interactions, discussing molecular tethers and looseners of LADs, and their link to transcription regulation and genome replication. It also provides a brief summary of technological advances that may uncover new aspects of LAD biology.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Cell Biology
Hiroshi Kimura, Yuko Sato
Summary: Recent advances in microscopy techniques have revealed the formation of transcription foci by RNA polymerase II (RNAP2) in the nucleus, which depend on its phosphorylation states. Spatially separated initiation and elongation foci have also been observed, suggesting the presence of transcription initiation and elongation factories.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Cell Biology
Satoshi Uchino, Yuma Ito, Yuko Sato, Tetsuya Handa, Yasuyuki Ohkawa, Makio Tokunaga, Hiroshi Kimura
Summary: A genetically encoded modification-specific intracellular antibody probe was developed to detect RNAP2 Ser2 phosphorylation in living cells, revealing its specific role in transcription complexes and providing insights into genome and cell function.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Developmental Biology
Tadayoshi Murakawa, Tsuyoshi Nakamura, Kohei Kawaguchi, Futoshi Murayama, Ning Zhao, Timothy J. Stasevich, Hiroshi Kimura, Naonobu Fujita
Summary: The research team has developed a versatile toolkit for Drosophila, using a genetically encoded single-chain variable fragment, to analyze the function of a protein of interest (POI) in live tissues. By crossing different tagged flies, various analyses of the tagged POI in vivo can be conducted. The study reveals that downregulated lysosomal function in the fat body plays a crucial role in the metamorphosis of Drosophila.
Article
Cell Biology
Yohei Kono, Stephen A. Adam, Yuko Sato, Karen L. Reddy, Yixian Zheng, Ohad Medalia, Robert D. Goldman, Hiroshi Kimura, Takeshi Shimi
Summary: The major structural component of nuclear lamina, lamin C, rapidly accumulates at sites of NE rupture, promoting repair. This accumulation is dependent on the immunoglobulin-like fold domain that binds to BAF and a nuclear localization signal, and is partly responsible for the accumulation of nuclear BAF and cytoplasmic cGAS.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Misako Tanaka, Hiroyuki Harada, Hiroshi Kimura
Summary: Carcinogenesis is often associated with alterations in histone modifications. This study investigated the levels of various histone modifications in different types of oral squamous cell carcinoma (OSCC) cell lines and found that a high level of H3K9me3 could be a marker of metastasis. Additionally, suppressing H3K9me3 through knockdown of SUV39H1 and SUV39H2 inhibited cell proliferation and migration, suggesting H3K9me3 as a potential therapeutic target for OSCC treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ksenia Kuznetsova, Noemie M. Chabot, Martino Ugolini, Edlyn Wu, Manan Lalit, Haruka Oda, Yuko Sato, Hiroshi Kimura, Florian Jug, Nadine L. Vastenhouw
Summary: The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. Proteins of the transcriptional machinery come together to form these bodies, but the process is not well understood. In this study, two large, isolated, and long-lived transcription bodies in zebrafish embryos were studied to characterize the dynamics of transcription body formation. The clustering of transcription factors, particularly Nanog and Sox19b, play a crucial role in initiating transcription and organizing these bodies.
Article
Cell & Tissue Engineering
Hiroki Ozawa, Azusa Kambe, Kodai Hibi, Satoshi Murakami, Akira Oikawa, Tetsuya Handa, Katsunori Fujiki, Ryuichiro Nakato, Katsuhiko Shirahige, Hiroshi Kimura, Nobuaki Shiraki, Shoen Kume
Summary: Human induced pluripotent stem cells (iPSCs) require high levels of methionine (Met) for maintaining pluripotency. Met deprivation leads to decreased levels of intracellular S-adenosyl-methionine (SAM), triggering differentiation and apoptosis of undifferentiated cells. Short-term Met deprivation affects the pluripotency network through epigenetic modifications, specifically on histone H3 trimethylation at lysine 4 (H3K4me3). The transcription start site (TSS) region of genes involved in transforming growth factor beta pathway, cholesterol biosynthetic process, as well as key pluripotent genes NANOG and POU5F1, are specifically affected by Met deprivation. Upon differentiation, loss of H3K27me3 occurs in many endodermal genes, leading to their activation and switching from a bivalent to a monovalent state (H3K4me3).
Article
Multidisciplinary Sciences
Hiroaki Ohishi, Seiru Shimada, Satoshi Uchino, Jieru Li, Yuko Sato, Manabu Shintani, Hitoshi Owada, Yasuyuki Ohkawa, Alexandros Pertsinidis, Takashi Yamamoto, Hiroshi Kimura, Hiroshi Ochiai
Summary: The authors developed a new tool called STREAMING-tag that can reveal the relationship between transcriptional activity and protein clusters, which is useful for quantitatively understanding transcriptional regulation in living cells.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Junya Adachi, Haruka Oda, Toshiaki Fukushima, Beni Lestari, Hiroshi Kimura, Hiroka Sugai, Kentaro Shiraki, Rei Hamaguchi, Kohei Sato, Kazushi Kinbara
Summary: Cell-imaging methods with functional fluorescent probes are widely used for evaluating physical parameters in cellular microenvironments. In this study, we developed viscosity-responsive fluorescent probes that are not dependent on the twisted intramolecular charge transfer (TICT) process. These probes showed enhanced fluorescence as the viscosity increased, allowing specific visualization of dense organelles in living cells under washout-free conditions. This research provides a new direction for developing functional fluorescent probes targeting dense organelles.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Fumiaki Nakamura, Hiroshi Kimura, Nobuhiro Fusetani, Yoichi Nakao
Summary: Two previously unreported onnamide analogs, 2Z- and 6Z-onnamides A (1 and 2), were isolated from the marine sponge Theonella conica collected at Amami-Oshima Is., Kagoshima Prefecture, Japan. The structures of compounds 1 and 2 were determined by spectoral analysis. They exhibited structure-activity relationships in histone modifications and cytotoxicity against HeLa and P388 cells.
Correction
Cell Biology
Adam Karoutas, Witold Szymanski, Tobias Rausch, Sukanya Guhathakurta, Eva A. Rog-Zielinska, Remi Peyronnet, Janine Seyfferth, Hui-Ru Chen, Rebecca de Leeuw, Benjamin Herquel, Hiroshi Kimura, Gerhard Mittler, Peter Kohl, Ohad Medalia, Jan O. Korbel, Asifa Akhtar
NATURE CELL BIOLOGY
(2023)
Article
Biology
Haruka Oda, Yuko Sato, Shigehiro A. Kawashima, Yusuke Fujiwara, Mate Palfy, Edlyn Wu, Nadine L. Vastenhouw, Motomu Kanai, Hiroshi Kimura
Summary: Filamentous actin (F-actin) in the cytoplasm plays a crucial role in cell regulation, and recent studies have discovered its association with various functions in the nucleus. By live imaging of zebrafish embryos, it was shown that F-actin accumulates in nuclei during the interphase and reaches a peak during the prophase. Even after the breakdown of the nuclear envelope, patches of F-actin remain near the condensing chromosomes. This accumulation of F-actin in the nucleus may contribute to proper mitotic progression in zebrafish embryos.
Article
Biochemistry & Molecular Biology
Hiroshi Ochiai, Hiroaki Ohishi, Yuko Sato, Hiroshi Kimura
Summary: Higher-order genomic structures and the formation of condensates around genes have been found to play important roles in regulating gene expression. Recent advancements in technology allow for the visualization of the dynamic spatiotemporal relationship between these structures and transcriptional activity in living cells.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Correction
Biochemical Research Methods
Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Shoko Sato, Masaru Nakao, Naoki Goto, Hitoshi Kurumizaka, Yasuyuki Ohkawa, Hiroshi Kimura
Article
Chemistry, Multidisciplinary
Yancen Dai, Yuko Sato, Bo Zhu, Tetsuya Kitaguchi, Hiroshi Kimura, Farid J. Ghadessy, Hiroshi Ueda
Summary: This study developed a conditionally active Q-body probe for precise imaging of intracellular p53 in living cells with low background signal. The Q-body showed significant fluorescence enhancement in vitro and in both fixed and live cells. Live-cell sorting based on p53 expression was also demonstrated.