Article
Chemistry, Physical
Goro Nishide, Keesiang Lim, Mahmoud Shaaban Mohamed, Akiko Kobayashi, Masaharu Hazawa, Takahiro Watanabe-Nakayama, Noriyuki Kodera, Toshio Ando, Richard W. Wong
Summary: The study utilized high-speed atomic force microscopy to observe dynamic DNA-histone H2A interactions, revealing different conformations on different substrates and observing reversible liquid-liquid phase separation of DNA-H2A aggregates.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Fritz Nagae, Shoji Takada, Tsuyoshi Terakawa
Summary: In this study, researchers found that partial unwrapping of a nucleosome by an RNA polymerase significantly facilitates the dismantling of an H2A/H2B dimer from the nucleosome by Nap1. The results also revealed the molecular mechanisms of Nap1 functions, in which the highly acidic C-terminal flexible tails of Nap1 contribute to the binding of H2A/H2B. These findings have important implications for understanding how histone chaperones process nucleosomes upon collisions with translocases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Food Science & Technology
Constanze Hesse, Helen C. Knight
Summary: Studies have shown that people have stronger cognitive, behavioral, and neurophysiological responses to palatable high-calorie foods compared to low-calorie foods. This is attributed to the higher incentive value of high-calorie foods, which triggers cravings and affects consumption. However, food cravings are not solely determined by intrinsic food properties, but also depend on extrinsic factors such as the physical availability of food items.
FOOD QUALITY AND PREFERENCE
(2023)
Article
Cell Biology
Julia M. Freewoman, Rajiv Snape, Feng Cui
Summary: The tumor suppressor protein p53, when activated, regulates the expression of target genes, with early genes showing clustering of p53 binding sites near gene starts and decreased nucleosome occupancy, while late genes have uniformly distributed p53 binding sites with increased nucleosome occupancy. This differential accessibility of p53 binding sites in nucleosomal context influences gene expression dynamics.
Review
Genetics & Heredity
Paul W. Hook, Winston Timp
Summary: Hook and Timp describe the flexible uses of single-molecule sequencing technologies in genome analysis, including targeted sequencing, chromatin state analysis, and sequencing of short reads. The matured high-throughput short-read sequencing technology has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, leading to a more accessible era of nucleic acid sequencing.
NATURE REVIEWS GENETICS
(2023)
Article
Multidisciplinary Sciences
David A. Bates, Charles E. Bates, Andrew S. Earl, Colin Skousen, Ashley N. Fetbrandt, Jordon Ritchie, Paul M. Bodily, Steven M. Johnson
Summary: This study confirms the phenomenon of end bias of in vitro nucleosomes and presents a method to recover nucleosomes which form towards the terminal ends of fragmented DNA. It is shown that although nucleosomes prefer to form on DNA ends, it does not skew results or their interpretation.
Article
Biochemical Research Methods
Tim Stuart, Avi Srivastava, Shaista Madad, Caleb A. Lareau, Rahul Satija
Summary: Signac is a comprehensive toolkit for the analysis of single-cell chromatin data, enabling end-to-end analysis and interoperability with the Seurat package for multimodal analysis.
Article
Biochemistry & Molecular Biology
Meiting Yang, Xiaorong Li, Zizi Tian, Lulu Ma, Jun Ma, Yunlong Liu, Guohui Shang, Ailing Liang, Wei Wu, Zhongzhou Chen
Summary: Recent research has discovered the MPND protein as a potential sensor for recognizing DNA 6mA modification in eukaryotes. Crystal structures of apo-MPND and MPND-DNA complex were determined, revealing dynamic assemblies. MPND was found to directly bind to histones and the interaction between MPND and histones was enhanced by DNA and the acidic regions of MPND. These findings provide structural information for further research on gene control and transcriptional regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Man Hsin Hung, Ching Wen Chang, Kathy Cheng Wang, Jittiporn Chaisaingmongkol, Mathuros Ruchirawat, Tim F. Greten, Xin Wei Wang
Summary: In this study, the researchers analyzed the purine metabolism pathways in tumor and non-tumor liver tissues of patients with hepatocellular carcinoma (HCC), one of the most lethal cancers globally. The findings showed that purine synthesis genes are upregulated and purine degradation genes are inhibited in HCC tumors. High purine anabolism is associated with specific somatic mutational signatures and leads to dysregulation of DNA damage repairing machinery. Furthermore, high purine anabolism determines the sensitivity of HCC to DDR-targeting agents and correlates with clinical outcomes.
Article
Biotechnology & Applied Microbiology
Vadim Fedyuk, Nir Erez, Noa Furth, Olga Beresh, Ekaterina Andreishcheva, Abhijeet Shinde, Daniel Jones, Barak Bar Zakai, Yael Mavor, Tamar Peretz, Ayala Hubert, Jonathan E. Cohen, Azzam Salah, Mark Temper, Albert Grinshpun, Myriam Maoz, Aviad Zick, Guy Ron, Efrat Shema
Summary: This study developed a single-molecule imaging technique that can accurately and sensitively detect colorectal cancer in cell-free nucleosomes. By analyzing the epigenetics, DNA methylation, and cancer-specific protein biomarkers of plasma-isolated nucleosomes, the system allows for high-resolution detection of histone modifications and provides quantitative data on plasma proteins. The analysis showed high accuracy and sensitivity in detecting cancer, even at early stages, and could determine the tissue origin of tumors.
NATURE BIOTECHNOLOGY
(2023)
Review
Endocrinology & Metabolism
Xiaoqiang Sun, Liu Wang, S. M. Bukola Obayomi, Zong Wei
Summary: Epigenetic signatures play a crucial role in defining beta cell identity during development and maintaining function in homeostatic states, but they are disrupted during the progression of T2DM.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Review
Plant Sciences
Tobias Jores, Morgan Hamm, Josh T. Cuperus, Christine Queitsch
Summary: Understanding plant gene regulation has been a long-standing challenge for plant scientists. Recent advancements in next-generation sequencing technology and computational approaches have provided new insights into the regulatory code of plants. This review discusses these methods and their contribution to our understanding of plant gene regulation.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Review
Immunology
Tianhao Xu, Renata M. Pereira, Gustavo J. Martinez
Summary: Naive CD8(+) T cells clonally expand and differentiate into distinct cell fates upon encountering their cognate antigen in vivo, regulated by transcription factors and epigenetic modulators. Multiple models have been proposed to explain the differentiation of CTLs, but none fully recapitulate the experimental evidence. This review article summarizes the latest research on the epigenetic regulation of CTL differentiation and presents a combined model to contemplate them.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tommy Stormberg, Yuri L. Lyubchenko
Summary: In this study, the structure and properties of CENP-A nucleosomes on DNA substrates were investigated using Atomic Force Microscopy. The findings suggest that DNA sequence and histone composition are important factors in accurate centromere assembly.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yang Yang, Liwei Zhang, Chaoyang Xiong, Jun Chen, Li Wang, Zengqi Wen, Juan Yu, Ping Chen, Yanhui Xu, Jingji Jin, Yong Cai, Guohong Li
Summary: The study reveals that HIRA complex not only helps with the incorporation of H3.3 in regulatory regions in mouse embryonic stem cells, but also collaborates with SRCAP to deposit H2A.Z onto the promoters, thereby determining the transcriptional potential of poised genes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Hongfang Qiu, Razvan V. Chereji, Cuihua Hu, Hope A. Cole, Yashpal Rawal, David J. Clark, Alan G. Hinnebusch
Article
Biochemistry & Molecular Biology
Razvan V. Chereji, Josefina Ocampo, David J. Clark
Article
Biochemistry & Molecular Biology
Razvan V. Chereji, Vasudha Bharatula, Nils Elfving, Jeanette Blomberg, Miriam Larsson, Alexandre V. Morozov, James R. Broach, Stefan Bjorklund
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Thomas A. Johnson, Razvan V. Chereji, Diana A. Stavreva, Stephanie A. Morris, Gordon L. Hager, David J. Clark
NUCLEIC ACIDS RESEARCH
(2018)
Review
Biophysics
Razvan V. Chereji, David J. Clark
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemistry & Molecular Biology
Ryota Ouda, Naoyuki Sarai, Vishal Nehru, Mira C. Patel, Maxime Debrosse, Mahesh Bachu, Razvan Chereji, Peter R. Eriksson, David J. Clark, Keiko Ozato
Article
Cell Biology
Yashpal Rawal, Razvan Chereji, Hongfang Qiu, Sudha Ananthakrishnan, Chhabi K. Govind, David J. Clark, Alan G. Hinnebusch
GENES & DEVELOPMENT
(2018)
Article
Biochemistry & Molecular Biology
Yashpal Rawal, Razvan V. Chereji, Vishalini Valabhoju, Hongfang Qiu, Josefina Ocampo, David J. Clark, Alan G. Hinnebusch
Article
Multidisciplinary Sciences
Pavel Khromov, Constantin D. Malliaris, Alexandre V. Morozov
Article
Biochemistry & Molecular Biology
Gunjan D. Mehta, David A. Ball, Peter R. Eriksson, Razvan Chereji, David J. Clark, James G. McNally, Tatiana S. Karpova
Article
Multidisciplinary Sciences
Han-Wen Chang, Maria E. Valieva, Alfiya Safina, Razvan Chereji, Jianmin Wang, Olga Kulaeva, Alexandre Morozov, Mikhail P. Kirpichnikov, Alexey Feofanov, Katerina Gurova, Vasily M. Studitsky
Article
Biochemistry & Molecular Biology
Josefina Ocampo, Razvan Chereji, Peter R. Eriksson, David J. Clark
Review
Biochemistry & Molecular Biology
Dorothea Tholl, Zarley Rebholz, Alexandre V. Morozov, Paul E. O'Maille
Summary: Many animals release terpenes as semiochemicals for inter- and intra-specific interactions. The biosynthetic origin of these compounds has remained unclear, but recent advances in genome and transcriptome resources have led to the identification of enzymes and pathways involved in independent terpene production. These findings have important implications for understanding terpene biosynthesis in animals and for developing applications in pharmaceuticals and agriculture.
NATURAL PRODUCT REPORTS
(2023)
Article
Physics, Multidisciplinary
Aditya Ballal, Willow B. Kion-Crosby, Alexandre Morozov
Summary: This paper presents an approach to partitioning network nodes into nonoverlapping communities, which is crucial for understanding network modularity and functional organization. By using random walks and the walk-likelihood algorithm, an optimal partition can be obtained, and the method has been successfully applied to a large-scale road and intersection map.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Razvan V. Chereji, Srinivas Ramachandran, Terri D. Bryson, Steven Henikoff