Article
Oncology
Yilin Deng, Jinjin Gao, Guangying Xu, Yuan Yao, Yan Sun, Yehui Shi, Xishan Hao, Liling Niu, Hui Li
Summary: This study found that HDAC6 is highly expressed in metastatic colon cancer tissues and inhibiting or silencing HDAC6 can suppress colon cancer metastasis. The study also revealed the interaction between HDAC6 and AKAP12, and the deacetylation and ubiquitination processes that lead to the degradation of AKAP12.
Article
Biochemistry & Molecular Biology
Roberto Amigo, Fernanda Raiqueo, Estefania Tarifeno, Carlos Farkas, Jose L. Gutierrez
Summary: The establishment and maintenance of nucleosome-free regions (NFRs) are essential processes in chromatin dynamics. This study investigates the role of transcription factors, chromatin remodeling complexes, and DNA sequences, particularly poly(dA:dT) tracts, in nucleosome remodeling. The results show that poly(dA:dT) tracts have differential effects on the activity of chromatin remodeling complexes and affect the directionality of nucleosome sliding. These findings shed light on the mechanisms underlying asymmetrical chromatin opening around poly(dA:dT) tracts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Vladyslava Sokolova, Shayan Sarkar, Dongyan Tan
Summary: Histone proteins play important roles in packaging genomic DNA and regulating gene accessibility. Recent cryoelectron microscope studies provide new insights into how histone variants influence the structures and functions of chromatin. This article reviews the current knowledge on histone variants biochemistry and discusses the implications of the new structural information on histone variant biology and their functions in transcription.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Charles Brobbey, Shasha Yin, Liu Liu, Lauren E. Ball, Philip H. Howe, Joe R. Delaney, Wenjian Gan
Summary: Protein arginine methyltransferase 5 (PRMT5) catalyzes methylation on arginine residues and has potential as an antitumor target. This study shows that autophagy blockage increases the sensitivity of triple negative breast cancer cells to PRMT5 inhibitor. PRMT5 mediates autophagy by methylating ULK1, and inhibition of ULK1 enhances the therapeutic effect of PRMT5 inhibitor. These findings suggest the combination of PRMT5 and autophagy inhibitors as a potential strategy in cancer therapy.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Jacob H. Martinsen, Daniel Saar, Catarina B. Fernandes, Benjamin Schuler, Katrine Bugge, Birthe B. Kragelund
Summary: Linker histone H1 plays a role in epigenetic regulation by binding to nucleosomes and altering chromatin structures. Recent research suggests that the number and position of charged side chains on the globular domain of H1 influence chromatin structure and gene repression. By analyzing charge variants of the globular domain, researchers found that modulating the number of charges has little effect on the structure, but affects the stability. This finding helps in understanding the function and structure of H1 histone.
Article
Multidisciplinary Sciences
Afshin Moradi, Martijn Wubs
Summary: The electrostatic theory of surface magnetoplasmons is extended to mixed Faraday-Voigt configurations, analyzing a strongly direction-dependent electrostatic surface wave that may be realized on narrow-gap semiconductors in the THz regime. The dispersion relation is presented along with its dependence on the applied magnetic field, showing that the group velocity is always perpendicular to the phase velocity. The velocity and energy relations of the magnetoplasmons are discussed in detail, with recovery of known surface magnetoplasmons in higher-symmetry Faraday and Voigt configurations in appropriate limits.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jiayi Fan, Andrew T. Moreno, Alexander S. Baier, Joseph J. Loparo, Craig L. Peterson
Summary: The study identifies three ATP-dependent phases in the H2A.Z deposition reaction, showing a complex pathway for timely and accurate deposition of H2A.Z at key genomic locations through ATP-dependent processes.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Yuhan Chang, Juan Zhang, Xinying Huo, Xinliang Qu, Chunlei Xia, Kaizong Huang, Fuyang Xie, Nuofan Wang, Xiaowei Wei, Qiong Jia
Summary: In this study, it is found that the F-actin regulator CRAD plays a negative role in the progression, stemness, and metastasis of colorectal cancer. Mechanistically, decreased CRAD in soft substrates enhances the stemness and metastasis potential of colorectal cancer by affecting the localization of YAP and the expression of stemness markers. Furthermore, CRAD deficiency also promotes colorectal tumor cell softening and epithelial-mesenchymal transition, contributing to its metastasis potential.
Article
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)
Article
Chemistry, Physical
Chiara Ricca, Ulrich Aschauer
Summary: Photochemical reactions on semiconductors are anisotropic, occurring at different rates on surfaces of different orientations. This study utilizes hybrid density functional theory to identify the surfaces associated with the majority of photo-generated carriers in various semiconductors. Spherical heat maps representing the probability of optical transitions at different wave vectors are created to predict the most reactive surfaces for photochemical applications. The research demonstrates a correlation between the heat maps and the anisotropy observed in conventional band structure plots, while highlighting the importance of considering all possible transitions for a comprehensive understanding.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Alexey V. V. Onufriev
Summary: The stability of protein-ligand complexes is sensitive to the pH of their environment. By computationally examining a set of protein-nucleic acid complexes, including the nucleosome, we found that an increase in intracellular/intra-nuclear pH destabilizes most complexes. We propose the use of ΔΔG(0.3) to quantify the effect, which represents the change in the binding free energy due to a pH increase of 0.3 units.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Cell Biology
Sebastian Eustermann, Avinash B. Patel, Karl-Peter Hopfner, Yuan He, Philipp Korber
Summary: ATP-dependent chromatin remodellers regulate chromatin transactions by re-arranging nucleosomes. Recent studies have elucidated the organization of remodeller complexes, their ATPase activity, their regulation and their pathological dysregulation.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kheerthana Duraivelan, Sagarika Dash, Dibyendu Samanta
Summary: Nectins, a family of cell surface glycoproteins, mediate cell-cell adhesion and signaling pathways, with specific heterophilic interactions dictating their physiological relevance.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Alessandra Feoli, Giulia Iannelli, Alessandra Cipriano, Ciro Milite, Lei Shen, Zhihao Wang, Andrea Hadjikyriacou, Troy L. Lowe, Cyrus Safaeipour, Monica Viviano, Giuliana Sarno, Elva Morretta, Maria Chiara Monti, Yanzhong Yang, Steven G. Clarke, Sandro Cosconati, Sabrina Castellano, Gianluca Sbardella
Summary: PRMT7 and PRMT9 have been identified as important therapeutic targets, but their biological roles, functions, and structural requirements are still unclear. This study discovered a potent PRMT7/9 inhibitor and revealed its binding mode to the two enzymes. The inhibition of PRMT activity in cells was confirmed, and an effective AlphaLISA assay was developed for screening small molecule inhibitors of PRMT9.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Review
Genetics & Heredity
Jasmita Gill, Anuj Kumar, Amit Sharma
Summary: Nucleosome assembly proteins (NAPs) play a central role in chromatin assembly and disassembly, and their interactions with histones are diverse and complex. Further research is needed to understand the dynamic nature of NAP-histone interactions.
EPIGENETICS & CHROMATIN
(2022)
Article
Biochemistry & Molecular Biology
Rauf Ahmad Najar, Nissar Ahmad Wani, Javeed Ahmad Bhat, Nawab John Dar, Beenish Rahat, Ajai Prakash Gupta, Jaspreet Kaur, Jyotdeep Kaur, Abid Hamid
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Laxmi Narayan Mishra, Jeffrey J. Hayes
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Parvaiz A. Dar, Sameer A. Mir, Javeed A. Bhat, Abid Hamid, Laishram R. Singh, Fayaz Malik, Tanveer A. Dar
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2019)
Article
Chemistry, Physical
Sohail A. Jalil, Mahreen Akram, Javeed A. Bhat, Jeffrey J. Hayes, Subhash C. Singh, Mohamed ElKabbash, Chunlei Guo
APPLIED SURFACE SCIENCE
(2020)
Article
Genetics & Heredity
Luke T. Marr, Josefina Ocampo, David J. Clark, Jeffrey J. Hayes
Summary: The study reveals that nucleosome surfaces within yeast chromatin are generally equally accessible throughout the genome, indicating a globally uncompacted chromatin structure lacking substantial higher-order organization. However, modest differences in accessibility were found, correlating with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible. Internal histone surfaces thought to be accessible in actively transcribed genes were not found to be appreciably exposed, indicating a rapid and efficient conversion of non-canonical nucleosome species to canonical structure in native chromatin.
EPIGENETICS & CHROMATIN
(2021)
Article
Microbiology
Sudisht Kumar Sah, Jeffrey Joseph Hayes, Elena Rustchenko
Review
Biochemistry & Molecular Biology
Luke T. Marr, Prasoon Jaya, Laxmi N. Mishra, Jeffrey J. Hayes
Summary: The article reviews decades of research efforts on defining the genome-wide chromatin landscape, from initial experiments showing discontinuities in chromatin structure related to gene activation to extensions using deep sequencing methods to elucidate general features of chromatin related to gene states. It also discusses chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Biochemical Research Methods
Fanfan Hao, Laxmi N. Mishra, Prasoon Jaya, Richard Jones, Jeffrey J. Hayes
Summary: Linker histones (H1s) are important for stabilizing chromatin structure and regulating transcription. The C-terminal domain (CTD) of H1 is involved in binding to chromatin and condensing upon nucleosome binding. Phosphorylation is a common modification in H1, but its specific effects and locations are unclear. Mass spectrometry techniques were used to identify phosphorylation sites in the CTD of linker histone Xenopus H1.0 and investigate its effects on chromatin structure.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Review
Pharmacology & Pharmacy
Javeed Ahmad Bhat, Tahira Akther, Rauf Ahmad Najar, Faheem Rasool, Abid Hamid
Summary: This article summarizes the potential properties and medicinal benefits of Withania somnifera (W. somnifera), commonly known as winter cherry or ashwagandha, especially in cancer and neurodegenerative diseases. It discusses the role of W. somnifera in DNA repair mechanisms and prevention of apoptosis in normal cells. The available data suggest that W. somnifera is effective in controlling disease progression and could be a potential therapeutic target. The article also addresses the traditional medicinal applications of W. somnifera and the obstacles that need to be overcome for its evaluation as a curative agent in humans.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Subhra Kanti Das, Ashok Kumar, Fanfan Hao, Amber R. Cutter Dipiazza, He Fang, Tae-Hee Lee, Jeffrey J. Hayes
Summary: The H1 C-terminal domain (CTD) undergoes distinct static and dynamic structural changes upon binding to nucleosomes, which can be decondensed through acetylation. The interactions between H1 CTD and linker DNA primarily occur between the first 30 residues of CTD and the first -25 bp of linker DNA.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Axel Poulet, Laxmi Narayan Mishra, Stephane Teletchea, Jeffrey J. Hayes, Yannick Jacob, Christophe Thiriet, Celine Duc
Summary: Histones in Physarum polycephalum are highly conserved, shedding light on the organism's position in the eukaryotic phylogeny. Studying histones contributes to a better understanding of the evolutionary history of Mycetozoans.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Fanfan Hao, Kevin J. Murphy, Tomoya Kujirai, Naoki Kamo, Junko Kato, Masako Koyama, Akimitsu Okamato, Gosuke Hayashi, Hitoshi Kurumizaka, Jeffrey J. Hayes
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Angela Balliano, Fanfan Hao, Catherine Njeri, Lata Balakrishnan, Jeffrey J. Hayes