Review
Virology
Boris Ryabchenko, Vojtech Sroller, Lenka Hornikova, Alexey Lovtsov, Jitka Forstova, Sandra Huerfano
Summary: This review provides detailed descriptions of the diverse and complex interactions between small and medium size DNA viruses and promyelocytic leukemia nuclear bodies (PM NBs). The interactions between PM NB components and viruses can influence viral genome expression and/or replication, as well as IFN-mediated or apoptotic cell responses to viral infection. The review also discusses the interactions between PM NBs and Hepatitis B virus, papillomaviruses, polyomaviruses, and avian anellovirus. Despite numerous studies on the functions of PM NBs in the context of viral infection, there are still gaps in our understanding of the fine interactions between viruses and the highly dynamic PM NBs, which require further investigation.
Article
Cell Biology
Andrew S. Belmont
Summary: This work reviews the progress in studying nuclear compartments, including nuclear structures, bodies, and chromosome domains. By comparing different research methods, particularly microscopy and genomics, we explore the evolving concept of nuclear compartments. Additionally, this review discusses the establishment and maintenance mechanisms of nuclear compartments, as well as their potential functions, such as the role of nuclear speckles in gene expression regulation.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Kayo Nozawa, Yoshimasa Takizawa, Leonidas Pierrakeas, Chizuru Sogawa-Fujiwara, Kazumi Saikusa, Satoko Akashi, Ed Luk, Hitoshi Kurumizaka
Summary: The canonical nucleosome is the major packaging unit of eukaryotic chromatin, and the H3-H4 octasome is a nucleosome-like particle with alternative histone stoichiometry. The structure of the H3-H4 octasome is flexible.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Jung Min Kim
Summary: Microtubules are key components of the cytoskeleton and play important roles in cellular processes and genome maintenance. This review highlights recent advances in understanding the role of microtubule dynamics in DNA damage response and repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Analytical
Esther L. Miriklis, Ashley M. Rozario, Eli Rothenberg, Toby D. M. Bell, Donna R. Whelan
Summary: Super-resolution microscopy techniques are well-suited for probing the nanoscale landscape of genomic function and dysfunction, offering high spatial resolution and single molecule localization advantages. These advances have provided unprecedented insights into DNA structure and function and enabled characterization of subpopulations within a single cell. Ongoing development and application of these interdisciplinary techniques will continue to expand the toolbox available for research into the nanoscale genomic landscape.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2021)
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
Biology
Myriam Scherer, Clarissa Read, Gregor Neusser, Christine Kranz, Anna K. Kuderna, Regina Mueller, Florian Full, Sonja Woerz, Anna Reichel, Eva-Maria Schilling, Paul Walther, Thomas Stamminger
Summary: PML nuclear bodies undergo rearrangement to form giant cages upon viral infection, trapping viral genomes and capsids, and providing a multilayered defense strategy against viral infections.
Review
Genetics & Heredity
Jamie Phipps, Karine Dubrana
Summary: DNA double-strand breaks (DSBs) are a harmful form of DNA damage that require robust repair mechanisms. The repair process is influenced by chromatin composition and dynamics, as well as 3D genome organization and break localization. The cohesin complex, involved in chromosome folding and sister chromatid cohesion, is emerging as a key player in DNA damage response, affecting repair pathway choice and efficiency.
Article
Energy & Fuels
Zhen Liu, Danliang Zhu, He Yang, Wendi Wang, Wenzhi Yang
Summary: This paper investigates the coal samples from four main mining areas in China with different metamorphic grades using nuclear magnetic resonance (NMR), mercury intrusion porosimetry (MIP), and scanning electron microscopy (SEM). The study examines the fissure-pore structure parameters and fractal characteristics of the coal bodies, revealing the influence of reservoir formation on the complexity of the coal body structure. The research results provide important scientific guidance for enhancing coalbed methane recovery and mine disaster prevention.
GEOMECHANICS FOR ENERGY AND THE ENVIRONMENT
(2022)
Article
Medicine, Research & Experimental
Laura M. Tsujikawa, Olesya A. Kharenko, Stephanie C. Stotz, Brooke D. Rakai, Christopher D. Sarsons, Dean Gilham, Sylwia Wasiak, Li Fu, Michael Sweeney, Jan O. Johansson, Norman C. W. Wong, Ewelina Kulikowski
Summary: The study reveals a new role for BET protein BRD4 in maintaining higher order chromatin structure at TADBs, highlighting the differential impact of BET inhibitors on TADB stability.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Seishiro Hirano, Osamu Udagawa
Summary: Promyelocytic leukemia (PML) proteins play a role in the development of acute promyelocytic leukemia (APL) and can be affected by trivalent arsenic (As3+). The exposure to As3+ can lead to changes in PML-NBs, including solubility shift, SUMOylation, and late agglomeration. Understanding these changes is important for the regulation of intranuclear dynamics of PML-NBs.
Article
Neurosciences
Yu-Han Chung, Qiu Qian, Hsin-Ying Huang, Wen-Tai Chiu, Chung-Shi Yang, Shun-Fen Tzeng
Summary: The study shows that overexpression of IL-33 in glioma cells can increase resistance to alkylating agents, possibly through upregulation of DNA repair genes. Conversely, IL-33 gene knockdown weakens abnormal nuclear characteristics in glioma cells, such as indentations and long clefts.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
Xuemei Cao, Cansu Kose, Christopher P. Selby, Aziz Sancar
Summary: The XR-seq method is widely used for mapping nucleotide excision repair genome-wide. It captures and sequences excised oligomers carrying DNA damage, and aligns their sequences to the genome. Researchers have successfully used ultraviolet light-irradiated plasmids as substrates for repair experiments in Escherichia coli and mammals, and found common excision product characteristics in both systems. This approach helps understand the effects of epigenetics and other cellular factors on DNA repair.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Miyu Sekiguchi, Nobuko Matsushita
Summary: This article provides a comprehensive overview of the role and regulatory mechanism of histone ubiquitination in DNA double-strand break repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Zhongwu Zhou, Rui Yan, Wen Jiang, Joseph M. K. Irudayaraj
Summary: The study reveals the hierarchical branching structure of chromatin, indicating a stepwise transition from compacted heterochromatin to dispersed euchromatin, providing important insights into the mechanism of higher order chromatin organization.
NANOSCALE ADVANCES
(2021)
Article
Hematology
Vinothkumar Rajan, Nicole Melong, Wing Hing Wong, Benjamin King, R. Spencer Tong, Nitin Mahajan, Daniel Gaston, Troy Lund, David Rittenberg, Graham Dellaire, Clinton J. V. Campbell, Todd Druley, Jason N. Berman
Article
Virology
Eric S. Pringle, Jaime Wertman, Nicole Melong, Andrew J. Coombs, Andrew L. Young, David O'Leary, Chansey Veinotte, Carolyn-Ann Robinson, Michael N. Ha, Graham Dellaire, Todd E. Druley, Craig McCormick, Jason N. Berman
Article
Ethics
Landon J. Getz, Graham Dellaire
SCIENCE AND ENGINEERING ETHICS
(2020)
Article
Biochemistry & Molecular Biology
Sabateeshan Mathavarajah, Carter VanIderstine, Graham Dellaire, Robert J. Huber
Summary: The model organism Dictyostelium discoideum provides insights into the evolution of unicellularity and multicellularity, aiding in the understanding of cancer-related gene networks. During development, Dictyostelium discoideum can form spore masses and stalk cells, with some cells sacrificing themselves. Cheating behaviors disrupt multicellularity principles and affect cell fate.
Article
Environmental Sciences
Sabateeshan Mathavarajah, Amina K. Stoddart, Graham A. Gagnon, Graham Dellaire
Summary: The ongoing COVID-19 pandemic has impacted public health, the economy, and society globally, with implications for the environment and wildlife. Poor wastewater management may lead to marine mammals being susceptible to infection by the SARS-CoV-2 virus through untreated wastewater discharge into natural water systems. Measures should be taken to prevent virus spillover in natural water systems to protect vulnerable marine wildlife populations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Genetics & Heredity
Kateryna Kratzer, Landon J. Getz, Thibaut Peterlini, Jean-Yves Masson, Graham Dellaire
Summary: Gene therapy for genetic diseases has gained increased attention, but faces technical challenges and ethical barriers. Current research is primarily focused on improving gene therapy and gene editing techniques, with less emphasis on the timing and rationale for using such technology.
Review
Cell Biology
J. P. Jose Merlin, H. P. Vasantha Rupasinghe, Graham Dellaire, Kieran Murphy
Summary: Cancer prevention and treatment involve multiple factors, including genetics, diet, DNA damage, and cell cycle regulation. Certain dietary components such as flavonoids and polyphenols can inhibit cancer progression through p53-mediated mechanisms. In addition, vitamins such as folic acid also play a significant role in chemoprevention.
OXIDATIVE MEDICINE AND CELLULAR LONGEVITY
(2021)
Review
Genetics & Heredity
Elias Habib, Allyson Cook, Sabateeshan Mathavarajah, Graham Dellaire
Summary: Autophagy is a crucial pathway for cellular homeostasis, with ESCRT proteins and alternative pre-mRNA splicing playing important roles in regulating this process. Dysfunction in these mechanisms can lead to impaired cellular stress response or trigger pathogenic reactions, ultimately contributing to human diseases.
Article
Oncology
Brianne M. Cruickshank, Marie-Claire D. Wasson, Justin M. Brown, Wasundara Fernando, Jaganathan Venkatesh, Olivia L. Walker, Fiorella Morales-Quintanilla, Margaret L. Dahn, Dejan Vidovic, Cheryl A. Dean, Carter VanIderstine, Graham Dellaire, Paola Marcato
Summary: This study demonstrates that lncRNA PART1 is enriched in triple-negative breast cancers and cancer stem cells, and is associated with worse outcomes in some breast cancer patients. PART1 alters the miRNA landscape, leading to genome-wide mRNA expression regulation, making it an attractive target for the treatment of triple-negative breast cancers.
Article
Biochemistry & Molecular Biology
Livia E. Clarke, Allyson Cook, Sabateeshan Mathavarajah, Amit Bera, Jayme Salsman, Elias Habib, Carter Van Iderstine, Moamen Bydoun, Stephen M. Lewis, Graham Dellaire
Summary: PRP4K is an essential gene that when reduced is associated with aggressive breast and ovarian cancer phenotypes, leading to increased cell migration and invasion. These effects suggest that PRP4K functions as a haploinsufficient tumor suppressor.
Article
Biochemistry & Molecular Biology
J. P. Jose Merlin, Graham Dellaire, Kieran Murphy, H. P. Vasantha Rupasinghe
Summary: Lung cancer has the highest mortality rate globally and is often diagnosed at late stages, necessitating genotoxic chemotherapy. Cancer prevention, including the use of antioxidants, is a major focus. The study found that an antioxidant formulation has the potential to reduce DNA damage, showing promise as a chemoprotectant by attenuating activation of kinase following carcinogen exposure.
Review
Genetics & Heredity
Elias B. Habib, Sabateeshan Mathavarajah, Graham Dellaire
Summary: Pre-mRNA processing factor 4 kinase (PRP4K) is a conserved kinase that plays important roles in spliceosomal assembly. However, recent studies have revealed that PRP4K is also involved in various cellular pathways, including transcription regulation, spindle assembly checkpoint, and tumor suppression, contributing to tumorigenesis and chemotherapy response.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Tharindu L. Suraweera, J. P. Jose Merlin, Graham Dellaire, Zhaolin Xu, H. P. Vasantha Rupasinghe
Summary: Cancer is a leading cause of death globally, but current treatments like chemotherapy and radiation therapy have significant side effects. Therefore, the prevention of cancer through dietary modifications has gained interest. This study examined the potential of selected flavonoids in reducing reactive oxygen species (ROS) and DNA damage induced by carcinogens through the activation of the Nrf2/ARE pathway. The results showed that genistein and PCB2 could effectively reduce ROS and DNA damage, and further research is needed to understand the role of dietary flavonoids in regulating the Nrf2/ARE pathway in carcinogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sabateeshan Mathavarajah, Graham Dellaire
Summary: The cGAS-STING pathway integrates DNA damage and cellular stress with type I interferon signaling, and the dysregulation of this pathway is associated with various diseases. L1 retroelements play a crucial role in the induction of cGAS-STING and interferon signaling. TREX1 is an important suppressor of cGAS-STING and L1 activity, and its loss leads to the accumulation of L1 retroelements.
BIOCHEMISTRY AND CELL BIOLOGY
(2023)
Article
Evolutionary Biology
Sabateeshan Mathavarajah, Andrew W. Thompson, Matthew R. Stoyek, T. Alexander Quinn, Stephane Roy, Ingo Braasch, Graham Dellaire
Summary: This study reveals that aquatic vertebrates undergo transcriptional rewiring of innate immune signaling pathways during limb and fin regeneration to promote immune cell recruitment. The study also shows that cGAS-STING pathway and various suppressors of cytosolic DNA play important roles in the regeneration process. The findings provide insights into the molecular mechanisms behind tissue regeneration in aquatic animals.
JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION
(2023)