Review
Cell Biology
Desmond J. Hamilton, Abigail E. Hein, Deborah S. Wuttke, Robert T. Batey
Summary: Nucleic acid binding proteins, specifically the high mobility group box (HMGB) proteins, have dual DNA and RNA binding abilities, allowing them to regulate gene expression. Through direct interaction with RNA, localization in RNA processing granules, and interactions with RNA binding proteins, HMGB proteins play crucial roles in protein-protein interactions, splicing outcomes, and genomic/cellular localization. Misregulation of HMGB-RNA interactions may also contribute to human diseases.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Multidisciplinary Sciences
Yuko Hasegawa, Kevin Struhl
Summary: The transcription factor SP1 exhibits varying binding dynamics at different target sites in the human genome, potentially influenced by factors such as location and cobinding factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Maria Theresia Watzlowik, Sujaan Das, Markus Meissner, Gernot Laengst
Summary: The gene transcription regulation of the human malaria parasite Plasmodium falciparum is governed by complex epigenetic mechanisms involving chromatin structure and dynamics. The high AT-content of the parasite genome and sequence divergence of chromatin-related proteins suggest significant differences in chromatin-dependent regulation compared to other eukaryotes. Specialized chromatin remodeling enzymes play an essential role in gene regulation in P. falciparum.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Hao Wu, Elise N. Munoz, Laura J. Hsieh, Un Seng Chio, Muryam A. Gourdet, Geeta J. Narlikar, Yifan Cheng
Summary: Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. The structures of Saccharomyces cerevisiae INO80 bound to a hexasome or a nucleosome reveal that INO80 binds the two substrates in substantially different orientations. The mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles.
Review
Biochemical Research Methods
Ricardo Andre Campos Ferraz, Ana Lucia Goncalves Lopes, Jessy Ariana Faria da Silva, Diana Filipa Viana Moreira, Maria Joao Nogueira Ferreira, Silvia Vieira de Almeida Coimbra
Summary: In the study of DNA-protein interactions, choosing the appropriate technique is crucial based on the objectives and capabilities of each research team. Different methods offer varying levels of precision and accuracy, requiring a comprehensive consideration of multiple options.
Article
Biochemistry & Molecular Biology
Jonna Heldrich, Carolyn R. Milano, Tovah E. Markowitz, Sarah N. Ur, Luis A. Vale-Silva, Kevin D. Corbett, Andreas Hochwagen
Summary: Successful meiotic recombination requires conserved axis proteins, which distribute on chromosomes through two independent pathways: a cohesin-dependent pathway and a cohesin-independent pathway. These pathways result in a stereotypic distribution pattern and the formation of chromatin islands that influence chromosome structure.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Xuezheng Wang, Yuantao Tang, Jiawei Xu, He Leng, Guojun Shi, Zaifeng Hu, Jiale Wu, Yuwen Xiu, Jianxun Feng, Qing Li
Summary: This study uncovers a new mechanism for parental histone recycling, revealing the important role of histone chaperone FACT and its N-terminus of the Spt16 subunit in budding yeast. The Spt16-N domain interacts with the replicative helicase MCM2-7, facilitating the formation of a critical ternary complex for efficient parental histone recycling and transfer to the lagging strand.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Uma P. Arora, Beth A. Sullivan, Beth L. Dumont
Summary: This study investigates the interplay between centromere variation and kinetochore protein sequence association in mice, and reveals strain-level differences in both CENP-A positioning and sequence preference along the core centromere satellite.
Review
Cell Biology
Brittany Cain, Brian Gebelein
Summary: Metazoans express multiple Hox transcription factors to specify cell fate along the anterior-posterior axis. Understanding how Hox factors regulate target genes for morphogenesis poses challenges on distinguishing their roles in activating/repressing genes for distinct segment identities and impacting organ development in a cell type-specific manner. Recent studies suggest Hox factors modify gene chromatin and utilize interactions with co-activators and co-repressors for accurate transcriptional outcomes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nadezhda S. Gerasimova, Nikolay A. Pestov, Vasily M. Studitsky
Summary: Transcription through nucleosomes by RNA polymerases (RNAP) is accompanied by the formation of small intranucleosomal DNA loops (i-loops), which are more efficiently formed in the presence of single-strand breaks or gaps in a non-template DNA strand (NT-SSBs). The presence of histone tails and NT-SSBs in linker DNA strongly facilitate the formation of i-loops during transcription of the promoter-proximal region of nucleosomal DNA, leading to the arrest of RNAP. DNA footprinting analysis supports the formation of an i-loop after stalling RNAP, indicating the involvement of histone tails and NT-SSBs in i-loop formation and arrest of RNAP during transcription.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Dominik Muehlen, Xiaojuan Li, Oleksandr Dovgusha, Herbert Jaeckle, Ufuk Guenesdogan
Summary: Epigenetic inheritance during DNA replication requires the assembly of nucleosomes from parental and newly synthesized histones. Lack of new histone synthesis leads to accessible chromatin, reduced nucleosome occupancy, and up-regulated and spurious transcription. However, the positions of modified parental histones are largely restored during DNA replication, suggesting recycling of parental histones to preserve the epigenetic landscape.
Article
Chemistry, Physical
Sujeet Kumar Mishra, Arnab Bhattacherjee
Summary: By developing a theoretical model based on a stochastic approach, the researchers investigated the target search mechanism of multiple Transcription Factors (TFs) on nucleosomal DNA. They analyzed when the TFs hierarchically search their binding motifs and when they simultaneously proceed via the formation of a protein-protein complex.
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)
Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Haibo Wang, Le Xiong, Patrick Cramer
Summary: TBP, a highly conserved protein, plays a central role in assembling the transcription preinitiation complex (PIC). TBP can bind to diverse nucleosome positions and its binding is stabilized by TFIIA. However, TBP-nucleosome complexes are incompatible with PIC assembly and must be removed before transcription initiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Masako Koyama, Hitoshi Kurumizaka
JOURNAL OF BIOCHEMISTRY
(2018)
Article
Cell Biology
Akihito Harada, Kazumitsu Maehara, Tetsuya Handa, Yasuhiro Arimura, Jumpei Nogami, Yoko Hayashi-Takanaka, Katsuhiko Shirahige, Hitoshi Kurumizaka, Hiroshi Kimura, Yasuyuki Ohkawa
NATURE CELL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Tomoya Kujirai, Haruhiko Ehara, Yuka Fujino, Mikako Shirouzu, Shun-ichi Sekine, Hitoshi Kurumizaka
Article
Multidisciplinary Sciences
Yasuhiro Arimura, Hiroaki Tachiwana, Hiroki Takagi, Tetsuya Hori, Hiroshi Kimura, Tatsuo Fukagawa, Hitoshi Kurumizaka
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Mariko Dacher, Hiroaki Tachiwana, Naoki Horikoshi, Tomoya Kujirai, Hiroyuki Taguchi, Hiroshi Kimura, Hitoshi Kurumizaka
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Yoshimasa Takizawa, Cheng-Han Ho, Hiroaki Tachiwana, Hideyuki Matsunami, Wataru Kobayashi, Midori Suzuki, Yasuhiro Arimura, Tetsuya Hori, Tatsuo Fukagawa, Melanie D. Ohi, Matthias Wolf, Hitoshi Kurumizaka
Review
Cell Biology
Hiroaki Tachiwana, Tatsuro Yamamoto, Noriko Saitoh
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2020)
Review
Oncology
Ryu-Suke Nozawa, Tatsuro Yamamoto, Motoko Takahashi, Hiroaki Tachiwana, Reo Maruyama, Toru Hirota, Noriko Saitoh
Review
Biochemistry & Molecular Biology
Hiroaki Tachiwana, Noriko Saitoh
Summary: LncRNAs are a class of non-coding RNAs widely present in mammalian cells, involved in regulating cellular functions. Their dysregulation in cancer is closely related to disease development and they have diagnostic and therapeutic potential.
CURRENT MEDICINAL CHEMISTRY
(2021)
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.
Article
Biochemistry & Molecular Biology
Shoko Sato, Yoshimasa Takizawa, Fumika Hoshikawa, Mariko Dacher, Hiroki Tanaka, Hiroaki Tachiwana, Tomoya Kujirai, Yukari Iikura, Cheng-Han Ho, Naruhiko Adachi, Indu Patwal, Andrew Flaus, Hitoshi Kurumizaka
Summary: Giardia lamblia forms a characteristic nucleosome core particle with asymmetric flexibility near the DNA entry-exit sites. Its octamer features a deeper acidic patch, and weaker associations between H2A-H2B and DNA with G. lamblia H3-H4 compared to human H3-H4. These findings suggest unrecognized capabilities for large scale sequence variations in eukaryotic chromatin organization.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Haruka Matsumori, Kenji Watanabe, Hiroaki Tachiwana, Tomoko Fujita, Yuma Ito, Makio Tokunaga, Kumiko Sakata-Sogawa, Hiroko Osakada, Tokuko Haraguchi, Akinori Awazu, Hiroshi Ochiai, Yuka Sakata, Koji Ochiai, Tsutomu Toki, Etsuro Ito, Ilya G. Goldberg, Kazuaki Tokunaga, Mitsuyoshi Nakao, Noriko Saitoh
Summary: In this study, the role of RPL5 in the nucleolus was defined using a machine learning algorithm. Lack of specific 60S ribosomal protein set led to nucleolar disintegration and unbundling of rDNA arrays. These findings contribute to the understanding of ribosomopathy.
LIFE SCIENCE ALLIANCE
(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.
Meeting Abstract
Oncology
Noriko Saitoh, Yuichi Ichikawa, Megumi Fukuoka, Hiroaki Tachiwana, Tatsuro Yamamoto
Article
Biology
Risa Fujita, Tatsuro Yamamoto, Yasuhiro Arimura, Saori Fujiwara, Hiroaki Tachiwana, Yuichi Ichikawa, Yuka Sakata, Liying Yang, Reo Maruyama, Michiaki Hamada, Mitsuyoshi Nakao, Noriko Saitoh, Hitoshi Kurumizaka
COMMUNICATIONS BIOLOGY
(2020)