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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)
Editorial Material
Oncology
Dragomir B. Krastev, Andrew J. Wicks, Christopher J. Lord
Summary: The study found that PARP inhibitors not only inhibit the catalytic activity of PARP1, but also trap it on DNA, leading to cytotoxicity in tumor cells. This discovery not only changed our understanding of how PARP inhibitors work, but also prompted further research on how PARP1 carries out its normal function in the absence of inhibitors.
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Chemistry, Multidisciplinary
Sevastyan O. Rabdano, Matthew D. Shannon, Sergei A. Izmailov, Nicole Gonzalez Salguero, Mohamad Zandian, Rudra N. Purusottam, Michael G. Poirier, Nikolai R. Skrynnikov, Christopher P. Jaroniec
Summary: The positively charged N-terminal histone tails interact with nucleosomal DNA, influencing their susceptibility to modifications and recognition by chromatin-binding proteins. The NMR data reveals that H4 tails are dynamically disordered in nucleosomes, showing a reduced conformational flexibility compared to free peptides. The findings suggest a fuzzy interaction between histone H4 tails and nucleosomal DNA, characterized by variable salt bridges and hydrogen bonds.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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Biochemistry & Molecular Biology
Alan Herbert, Fedor Pavlov, Dmitrii Konovalov, Maria Poptsova
Summary: The classical view of gene regulation draws from prokaryotic models and includes operons regulated by protein-DNA interactions. However, it is now known that operons can also be modulated by small RNAs. In eukaryotes, microRNAs (miR) and flipons play a crucial role in regulating gene expression. This study provides evidence of a deep connection between miR and flipon-based mechanisms and explores their interactions and influences on gene regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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Biology
Drake A. Donovan, Johnathan G. Crandall, Vi N. Truong, Abigail L. Vaaler, Thomas B. Bailey, Devin Dinwiddie, Orion G. B. Banks, Laura E. McKnight, Jeffrey N. McKnight
Summary: The study revealed that Isw2 functions as an obligately targeted nucleosome remodeler in vivo by interacting physically with sequence-specific factors. These data support an 'interacting barrier model' where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.
Review
Plant Sciences
Michal Lieberman-Lazarovich, Eirini Kaiserli, Etienne Bucher, Velimir Mladenov
Summary: This review summarizes the importance of utilizing epigenetic regulation in crop responses to environmental factors and optimizing yield, and discusses the feasibility of crop improvement through the use of epigenetic features.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Chalmers Chau, Fabio Marcuccio, Dimitrios Soulias, Martin Andrew Edwards, Andrew Tuplin, Sheena E. Radford, Eric Hewitt, Paolo Actis
Summary: This study presents a polymer-electrolyte solid-state nanopore system for analyzing biomolecular conformation under physiological conditions. By using specific salts, the system's performance is enhanced, allowing for the analysis of Chikungunya virus RNA conformation.
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Veterinary Sciences
Zhu Caiye, Shuzhen Song, Minna Li, Xaioyu Huang, Yan Luo, Suli Fang
Summary: The study aimed to analyze genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which have different tail types, and identify the differentially methylated genes (DMGs) affecting tail type. Whole genome bisulfite sequencing (WGBS) was used to detect three individuals from each breed, and the degree of methylation, differentially methylated regions (DMRs) and DMGs were analyzed. Functional analysis revealed several genes involved in fat metabolism, such as NFATC4, LPIN2, MGAT2 and MAT2B. These findings provide new insights into the epigenetic regulation mechanisms of fat deposition in sheep tails and contribute to the study of local sheep.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Paul Talbert, Steven Henikoff
Summary: A new study reveals that holocentromeres in certain plants and animals have an impact on genomic architecture, epigenome organization, and karyotype evolution.
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Nanoscience & Nanotechnology
Valery V. Prokhorov, Nikolay A. Barinov, Kirill A. Prusakov, Evgeniy Dubrovin, Maxim D. Frank-Kamenetskii, Dmitry Klinov
Summary: The study observed that DNA molecules adsorbed on a monomolecular film comprising charged lamellar templates can undergo sharp discontinuous kinks, local melting, and supercoiling. These structural anomalies are induced by lateral surface forces and the highly anisotropic electrostatic interaction between DNA and the underlying rows of positive surface charges. The results indicate a nonlinear mechanical response of DNA to lateral electrostatic stress at the nanoscale, beyond the scope of the worm-like chain approximation.
NANO-MICRO LETTERS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Patricia M. Di Lorenzo
Summary: In vivo two photon calcium imaging in the gustatory cortex of alert mice shows that taste-responsive cells can vary in their breadth of tuning across taste qualities and are sparse and spatially distributed across the cortex.
Article
Chemistry, Physical
Konstantin Roder
Summary: The study explores the potential and free energy landscape of histone tails, revealing a set of distinct structural ensembles crucial for the formation of liquid-like chromatin organization. The presence of multiple structures on a multifunnel energy landscape may be associated with multifunctionality.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Summary: A recent study revealed that Dnmt1 is activated by specific types of two-mono-ubiquitinated histone H3 tails, which plays a crucial role in cell maintenance. Molecular dynamics simulations showed that H3T acts as a spacer, inhibiting ubiquitin-ubiquitin intermolecular interactions and enhancing the binding to Dnmt1.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Cell & Tissue Engineering
Shumin Zhou, Juan Dong, Mengneng Xiong, Shiming Gan, Yujiao Wen, Jin Zhang, Xiaoli Wang, Shuiqiao Yuan, Yaoting Gui
Summary: UHRF1 plays a crucial role in regulating spermatogonial stem cells in mice, and its deficiency can lead to male infertility. In addition, UHRF1 can act as an RNA splicing regulator and participate in gene expression regulation. These findings provide important clues for treating human male infertility.
Review
Psychiatry
Iris Salamon Arcan, Katarina Kouter, Alja Videtic Paska
Summary: Depressive disorder is a complex disease that affects millions of people worldwide. Genetic, environmental, and neurobiological factors contribute to its development. DNA methylation, particularly in genes related to brain-derived neurotrophic factor, glucocorticoid receptor, and serotonin transporter, is a well-studied epigenetic modification in depressive disorder. Further research is needed to identify biomarkers for diagnosis and treatment response in clinical settings, including studying the effects of antidepressants on epigenetic changes throughout the genome.
WORLD JOURNAL OF PSYCHIATRY
(2022)
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Biochemistry & Molecular Biology
Qiong Tong, Gaofeng Cui, Maria Victoria Botuyan, Scott B. Rothbart, Ryo Hayashi, Catherine A. Musselman, Namit Singh, Ettore Appella, Brian D. Strahl, Georges Mer, Tatiana G. Kutateladze
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Immunology
Shaojun Xing, Fengyin Li, Zhouhao Zeng, Yunjie Zhao, Shuyang Yu, Qiang Shan, Yalan Li, Farrah C. Phillips, Peterson K. Maina, Hank H. Qi, Chengyu Liu, Jun Zhu, R. Marshall Pope, Catherine A. Musselman, Chen Zeng, Weiqun Peng, Hai-Hui Xue
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Biotechnology & Applied Microbiology
Katie S. Flenker, Elliot L. Burghardt, Nirmal Dutta, William J. Burns, Julia M. Grover, Elizabeth J. Kenkel, Tyler M. Weaver, James Mills, Hyeon Kim, Lingyan Huang, Richard Owczarzy, Catherine A. Musselman, Mark A. Behlke, Bradley Ford, James O. McNamara
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Multidisciplinary Sciences
Emma A. Morrison, Julio C. Sanchez, Jehnna L. Ronan, Daniel P. Farrell, Katayoun Varzavand, Jenna K. Johnson, Brian X. Gu, Gerald R. Crabtree, Catherine A. Musselman
NATURE COMMUNICATIONS
(2017)
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Biology
Emma A. Morrison, Samuel Bowerman, Kelli L. Sylvers, Jeff Wereszczynski, Catherine A. Musselman
Review
Biochemistry & Molecular Biology
Tyler M. Weaver, Emma A. Morrison, Catherine A. Musselman
Article
Biochemistry & Molecular Biology
Katelyn E. Connelly, Tyler M. Weaver, Aktan Alpsoy, Brian X. Gu, Catherine A. Musselman, Emily C. Dykhuizen
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Catherine A. Musselman, Tatiana G. Kutateladze
ACS CHEMICAL BIOLOGY
(2019)
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Microbiology
Mrutyunjaya Parida, Kyle A. Nilson, Ming Li, Christopher B. Ball, Harrison A. Fuchs, Christine K. Lawson, Donal S. Luse, Jeffery L. Meier, David H. Price
Article
Multidisciplinary Sciences
Tyler M. Weaver, Jiachen Liu, Katelyn E. Connelly, Chris Coble, Katayoun Varzavand, Emily C. Dykhuizen, Catherine A. Musselman
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Emma A. Morrison, Lokesh Baweja, Michael G. Poirier, Jeff Wereszczynski, Catherine A. Musselman
Summary: Hexasomes and tetrasomes are key intermediates in nucleosome assembly and disassembly, whose formation is regulated by histone chaperones and other factors. Changes in nucleosome composition, including the H3 tail conformation, can potentially impact chromatin signaling and landscape, suggesting a regulatory role in gene expression. The dynamic interactions between histone tails and DNA within these structures may play a significant role in chromatin function and gene regulation.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Catherine A. Musselman, Tatiana G. Kutateladze
Summary: The spatial and temporal modulation of chromatin structure is crucial for regulating DNA templated processes, and the nucleosome, as the basic subunit of chromatin, plays a key role in this regulation. Recent studies using NMR spectroscopy have revealed the atomic level conformation and dynamics of the nucleosome and provided a better understanding of the importance of these dynamics in key regulatory events.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Saumya M. De Silva, Alisha Dhiman, Surbhi Sood, Kilsia F. Mercedes, William J. Simmons, Morkos A. Henen, Beat Vogeli, Emily C. Dykhuizen, Catherine A. Musselman
Summary: PBRM1 is a subunit of the PBAF chromatin remodeling complex and is frequently mutated in clear cell renal cell carcinoma patients. It functions as a chromatin binding subunit and contains six tandem bromodomains which can bind nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). In addition, the second and fourth bromodomains of PBRM1 also have the ability to bind double stranded RNA elements.
NUCLEIC ACIDS RESEARCH
(2023)