Article
Biology
Elizabeth T. Wiles, Colleen C. Mumford, Kevin J. McNaught, Hideki Tanizawa, Eric U. Selker
Summary: Establishing and maintaining appropriate gene repression is crucial for multicellular organisms. H3K27 methylation is a common modification associated with gene repression, and recent research has identified the involvement of ISWI and ACF1 genes in the repression of H3K27-methylated genes in the filamentous fungus Neurospora crassa. These genes form an ACF chromatin-remodeling complex and interact with chromatin throughout the genome. Proper nucleosome positioning is critical for the repression of H3K27-methylated genes.
Review
Cell Biology
Aidan J. Levinsky, Gregor McEdwards, Nasha Sethna, Mark A. Currie
Summary: H3K9 methyltransferases play crucial roles in genome stability, cell type-specific gene expression, and non-histone methylation. They are involved in histone modification and regulate the methylation of various non-histone targets, contributing to genome regulation and cellular functions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biophysics
Jekabs Krigerts, Kristine Salmina, Talivaldis Freivalds, Pawel Zayakin, Felikss Rumnieks, Inna Inashkina, Alessandro Giuliani, Michael Hausmann, Jekaterina Erenpreisa
Summary: Researchers used MCF-7 breast cancer cells model to show that PADs may regulate gene expression by altering chromatin structure after treatment with heregulin (HRG), playing a crucial role in cell differentiation and re-patterning process.
BIOPHYSICAL JOURNAL
(2021)
Article
Biology
Sujeet Kumar Mishra, Kunhe Li, Simon Brauburger, Arnab Bhattacherjee, Nestor Norio Oiwa, Dieter W. Heermann
Summary: Nucleosome positioning plays a crucial role in important biological processes and can be used to predict genome function and chromatin organization. This study developed a theoretical model to analyze nucleosome positioning data and obtained genome-wide clustering in Candida albicans. The clustering revealed different nucleosome distributions and gene densities that govern differential gene expression patterns. Furthermore, these distribution patterns were conserved throughout the genome and within species.
Article
Cell Biology
Chao Zhang, Xuebin Zhang, Li Huang, Yiting Guan, Xiaoke Huang, Xiao-Li Tian, Lijun Zhang, Wei Tao
Summary: The study revealed a massive redistribution of chromatin accessibility in human umbilical vein endothelial cell (HUVEC) senescence, with AP-1 transcription factor family identified as crucial in driving this chromatin accessibility reconstruction. The remodeling of chromatin accessibility by AP-1 contributes to the senescence program, particularly through changes in intergenic chromatin regions. Additionally, ATF3 was found to be critical in promoting cellular senescence by reconstructing chromatin accessibility.
Article
Biochemical Research Methods
Parker Knight, Marie-Pierre L. Gauthier, Carolina E. Pardo, Russell P. Darst, Kevin Kapadia, Hadley Browder, Eliza Morton, Alberto Riva, Michael P. Kladde, Rhonda Bacher
Summary: Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methylscaper is a visualization framework that allows simultaneous analysis of DNA methylation and chromatin accessibility landscapes at the single-molecule or single-cell level. It implements a weighted principal component analysis that orders DNA molecules and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation, showing utility in identifying biologically relevant chromatin features while scaling to larger datasets.
Article
Biochemistry & Molecular Biology
Agnes Mendonca, Oscar F. Sanchez, Junkai Xie, Ana Carneiro, Li Lin, Chongli Yuan
Summary: Heterochromatin plays a crucial role in regulating gene expression and cell functionality. Its dynamic nature during the cell cycle and differentiation processes necessitates the development of live cell compatible tools for stable tracking. In this study, small recombinant protein probes are utilized to dynamically monitor heterochromatin changes induced by drug perturbations at the single cell level, showing promise for future research in this area.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Multidisciplinary Sciences
Iris Muller, Ann Sophie Moroni, Daria Shlyueva, Sudeep Sahadevan, Erwin M. Schoof, Aliaksandra Radzisheuskaya, Jonas W. Hojfeldt, Tulin Tatar, Richard P. Koche, Chang Huang, Kristian Helin
Summary: Deciphering the mechanisms controlling pluripotent ground state is crucial in understanding embryonic development. MPP8, an epigenetic protein, has been identified as essential for maintaining ground-state pluripotency through repression of LINE1 elements, independent of chromatin binding or H3K9me3 levels.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Clara Lopes Novo, Emily Wong, Colin Hockings, Chetan Poudel, Eleanor Sheekey, Meike Wiese, Hanneke Okkenhaug, Simon J. Boulton, Srinjan Basu, Simon Walker, Gabriele S. Kaminski Schierle, Geeta J. Narlikar, Peter J. Rugg-Gunn
Summary: The authors demonstrate that satellite transcripts in mouse embryonic stem cells play a role in driving the formation of HP1α droplets and modulating the organization of heterochromatin. Depleting these transcripts leads to a less dynamic and more static state of heterochromatin and results in chromosome instability. This study highlights the importance of satellite transcripts in maintaining genome stability.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Alejandra Agredo, Andrea L. Kasinski
Summary: Chromatin is regulated by histone proteins through various post-translational modifications, especially tri-methylation of histone H4 on lysine 20 (H4K20me3), which plays important roles in chromatin structure, cell cycle, DNA repair, and development. Recent studies have provided insights into the establishment and regulation of H4K20me3 and its involvement in various diseases through interactions with other proteins. This review aims to summarize the current knowledge of H4K20me3 function and regulation, as well as highlight remaining gaps in the field.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Maria Vaquero-Sedas, Miguel A. Vega-Palas
Summary: Telomeric regions in Arabidopsis have a bimodal chromatin structure, with telomeres lacking both euchromatic and heterochromatic marks, followed by heterochromatic subtelomeres. The presence of heterochromatic modifications in subtelomeres may play a significant role in telomere biology.
Article
Biology
Hiroaki Tachiwana, Mariko Dacher, Kazumitsu Maehara, Akihito Harada, Yosuke Seto, Ryohei Katayama, Yasuyuki Ohkawa, Hiroshi Kimura, Hitoshi Kurumizaka, Noriko Saitoh
Summary: The RhIP assay was developed to study the targeting of histone variants to the genome in eukaryotes. The study showed that H3.1, H3.3, H2A, and H2A.Z are incorporated into chromatin in different manners, and that chromatin structure and DNA replication play crucial roles in determining histone deposition for maintaining epigenetic chromatin states.
Review
Plant Sciences
Ruth Y. Akinmusola, Catherine-Axa Wilkins, James Doughty
Summary: Epigenetic modifications, especially DNA methylation, are critical for gene regulation and TE silencing. DDM1 is a chromatin remodeler that plays a central role in histone modifications and DNA methylation. It not only maintains the epigenome, but also regulates important plant traits such as flowering time and heterosis. DDM1's TE silencing mechanism is distinct and independent of other pathways, and is strongly associated with histone H1 and histone variant H2A.W. The DDM1-H2A.W strategy effectively silences mobile TEs and preserves genome stability.
Article
Biochemistry & Molecular Biology
Margaux Olivier, Amy Hesketh, Marie-Noelle Pouch-Pelissier, Thierry Pelissier, Ying Huang, David Latrasse, Moussa Benhamed, Olivier Mathieu
Summary: Transcriptional silencing is a crucial mechanism for gene expression control, and it is regulated by specific epigenetic marks on chromatin. This study demonstrates that the DNA helicase RTEL1 has an important role in transcriptional silencing. RTEL1 deficiency leads to upregulation of genes enriched in H3K27me3 mark, decreased DNA methylation, and hypermethylation and increased H3K27me3 in heterochromatin. Additionally, RTEL1 is involved in stabilizing DNA methylation and H3K27me3 patterns. These findings highlight the previously unappreciated roles of RTEL1 in transcriptional silencing.
NUCLEIC ACIDS RESEARCH
(2023)
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
Biochemistry & Molecular Biology
Qianmei Wu, Takeru Fujii, Akihito Harada, Kosuke Tomimatsu, Atsuko Miyawaki-Kuwakado, Masatoshi Fujita, Kazumitsu Maehara, Yasuyuki Ohkawa
Summary: The study found that MyoD-bound genome regions exhibit elevated levels of active histone modifications during the cell cycle, with H3K4me1/2/3 and H3K27ac being the key modifications. Additionally, it was shown that H3K4me2/3 levels remained elevated throughout the cycle, while H3K27ac and H3K4me1 levels decreased to levels similar to MyoD-unbound regions in later phases. The results suggest that MyoD binding forms selective epigenetic memories with H3K4me2/3 during the cell cycle, in addition to inducing myogenic genes through active chromatin formation and transcription.
JOURNAL OF BIOCHEMISTRY
(2021)
Article
Biology
Rina Hirano, Yasuhiro Arimura, Tomoya Kujirai, Mikihiro Shibata, Aya Okuda, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka
Summary: Hirano et al. demonstrate that the H2A.B-H2B histone dimer within the nucleosome exchanges with the canonical H2A-H2B dimer independently of histone chaperones or nucleosome remodelers. This study sheds light on the mechanism by which the H2A.B nucleosome exchanges its histones.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biology
Cheng-Han Ho, Yoshimasa Takizawa, Wataru Kobayashi, Yasuhiro Arimura, Hiroshi Kimura, Hitoshi Kurumizaka
Summary: SET8 is responsible for the mono-methylation of histone H4 lysine-20 (H4K20) in nucleosomes, and it specifically binds the nucleosomal acidic patch through an arginine anchor composed of Arg188 and Arg192 residues to achieve this function.
LIFE SCIENCE ALLIANCE
(2021)
Article
Biochemistry & Molecular Biology
Hideaki Ohtomo, Jun-ichi Kurita, Shun Sakuraba, Zhenhai Li, Yasuhiro Arimura, Masatoshi Wakamori, Yasuo Tsunaka, Takashi Umehara, Hitoshi Kurumizaka, Hidetoshi Kono, Yoshifumi Nishimura
Summary: The nucleosome is composed of histone dimers and tetramers, along with DNA, and the dynamic structures of H2A and H2B tails have been studied using NMR and molecular dynamics simulations, revealing different conformations in each nucleosome.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
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
Cell Biology
Daniel A. Bartlett, Vishnu Dileep, Tetsuya Handa, Yasuyuki Ohkawa, Hiroshi Kimura, Steven Henikoff, David M. Gilbert
Summary: The study introduces a high-throughput single-cell DNA binding site mapping method, TIP-seq, that is simple, cost-effective, and capable of multiplexing multiple samples per experiment.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kazumitsu Maehara, Kosuke Tomimatsu, Akihito Harada, Kaori Tanaka, Shoko Sato, Megumi Fukuoka, Seiji Okada, Tetsuya Handa, Hitoshi Kurumizaka, Noriko Saitoh, Hiroshi Kimura, Yasuyuki Ohkawa
Summary: Advancements in genome-wide technologies allow for analyses of cellular dynamics at the tissue level, with the ChIL-based approach providing high-depth epigenomic data. This method can generate reproducible epigenomic profiles from various tissue types, aiding in the evaluation of cell populations and gene activation in tissues. Integrative analyses using ChIL offer insights into the in vivo cell-type dynamics of tissues.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yoko Hayashi-Takanaka, Yuichiro Hayashi, Yasuhiro Hirano, Atsuko Miyawaki-Kuwakado, Yasuyuki Ohkawa, Chikashi Obuse, Hiroshi Kimura, Tokuko Haraguchi, Yasushi Hiraoka
Summary: During the G1 phase of the cell cycle, the MCM hexamer transitions from a single hexamer to a double hexamer, influencing the progression of the cell cycle. The methylation levels of histone H4K20 are correlated with the formation of the double MCM hexamer, leading to cell cycle arrest.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yasuhiro Arimura, Hironori Funabiki
Summary: In this study, cryo-EM structures of the Xenopus laevis egg A2M homolog tetramer were reported, revealing the structural basis behind the protease cleavage-induced global structural transformation and protease entrapment.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Keita Kohno, Ryoji Shirasaka, Kohei Yoshihara, Satsuki Mikuriya, Kaori Tanaka, Keiko Takanami, Kazuhide Inoue, Hirotaka Sakamoto, Yasuyuki Ohkawa, Takahiro Masuda, Makoto Tsuda
Summary: This study reveals the role of CD11c-expressing spinal microglia in the remission and recurrence of neuropathic pain. These microglia express IGF1, and interference with IGF1 signaling impairs pain recovery. Depletion of CD11c(+) microglia or interruption of IGF1 signaling leads to relapse in pain hypersensitivity.
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
Biology
Thomas Fleming, Yukiko Kikuchi, Mikoto Nakajo, Masaya Tachizawa, Tomoaki Inazumi, Soken Tsuchiya, Yukihiko Sugimoto, Daisuke Saito, Mikita Suyama, Yasuyuki Ohkawa, Takashi Baba, Ken-ichirou Morohashi, Kataaki Okubo
Summary: In Japanese rice fish, the prostaglandin E-2/ptger4b signaling pathway regulates the activity of FeSP neurons and female receptivity to male courtship.
COMMUNICATIONS BIOLOGY
(2022)
Review
Cell Biology
Tomoya Kujirai, Haruhiko Ehara, Shun-ichi Sekine, Hitoshi Kurumizaka
Summary: In eukaryotes, genomic DNA is packaged into chromatin and the nucleosome acts as a barrier to transcription. The RNA polymerase II elongation complex disassembles the nucleosome during transcription to allow passage. After transcription, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly, which plays a crucial role in preserving epigenetic information. The histone chaperone FACT is involved in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies have provided insights into the structural transitions of the nucleosome during transcription.
Article
Biochemistry & Molecular Biology
Seiya Hirai, Tomoya Kujirai, Munetaka Akatsu, Mitsuo Ogasawara, Haruhiko Ehara, Shun-ichi Sekine, Yasuyuki Ohkawa, Yoshimasa Takizawa, Hitoshi Kurumizaka
Summary: H3.8 is a non-allelic human histone variant derived from H3.3, forming an unstable nucleosome with more accessible entry/exit DNA regions compared to H3.3. This leads to altered RNAPII transcription profiles.
JOURNAL OF BIOCHEMISTRY
(2023)
Correction
Biochemical Research Methods
Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Shoko Sato, Masaru Nakao, Naoki Goto, Hitoshi Kurumizaka, Yasuyuki Ohkawa, Hiroshi Kimura
