Article
Multidisciplinary Sciences
Benjamin M. Spector, Mrutyunjaya Parida, Ming Li, Christopher B. Ball, Jeffery L. Meier, Donal S. Luse, David H. Price
Summary: Interactions between the RNA polymerase II preinitiation complex (PIC) and paused early elongation complexes with the +1 nucleosome are functionally important. However, there are differences in these interactions between cellular chromatin and the human cytomegalovirus (HCMV) genome. Host PICs and paused Pol II complexes frequently interact with the +1 nucleosome, while viral transcription complexes have limited nucleosomal interactions.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Imon Goswami, Poorva Sandlesh, Aimee Stablewski, Ilya Toshkov, Alfiya F. Safina, Mikhail Magnitov, Jianmin Wang, Katerina Gurova
Summary: This study highlights the importance of nucleosome maintenance during transcription and suggests that the histone chaperone FACT plays a role in preserving chromatin integrity in mammalian adult stem cells.
Article
Biochemistry & Molecular Biology
Ashutosh Shukla, Pratibha Bhalla, Pooja Kiran Potdar, Preethi Jampala, Purnima Bhargava
Summary: The FACT complex plays a role in regulating gene expression by influencing nucleosomal organization and controlling terminator-dependent Pol III transcription. Under different stress conditions, FACT shows differential enrichment patterns and gene-specific dynamics, offering a novel stress-sensing mechanism for transcription regulation.
Article
Critical Care Medicine
Sarah K. Medeiros, Neha Sharma, Dhruva Dwivedi, Patricia C. Liaw
Summary: This study investigates the cytotoxic effects of nucleosomes, DNA, and histones in vitro and in vivo. It is found that DNA masks the harmful effects of histones both in vitro and in vivo. Administration of histones contributes to the pathogenesis of sepsis, but nucleosomes or DNA injection is not harmful to healthy or septic mice.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Biochemistry & Molecular Biology
Jesus Beltran-Garcia, Juan J. Manclus, Eva M. Garcia-Lopez, Nieves Carbonell, Jose Ferreres, Maria Rodriguez-Gimillo, Concepcion Garces, Federico Pallardo, Jose L. Garcia-Gimenez, Angel Montoya, Carlos Roma-Mateo
Summary: The study evaluated the potential of chromatin-related biomarkers in decision making and outcome prediction, with HMGB1/citrullinated H3 determination in plasma showing the most promising clinical tool for monitoring and stratifying septic patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Amala Kaja, Abhinav Adhikari, Saswati Karmakar, Wanwei Zhang, Gerson Rothschild, Uttiya Basu, Surinder K. Batra, Judith K. Davie, Sukesh R. Bhaumik
Summary: The study reveals that human SPT16 is regulated by the proteasome, impacting the transcription of cancer-associated genes, and degradation of SPT16 is impaired in kidney cancer cells, leading to its upregulation.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alex Pablo-Kaiser, McKenzie G. Tucker, Grace A. Turner, Elijah G. Dilday, Avery G. Olmstead, Caroline L. Tackett, Andrea A. Duina
Summary: Recent studies have found an association between the L61R substitution in human histone H3.3 protein and neurodevelopmental disorders. This substitution, encoded by one allele of the H3F3A gene, may act in a dominant fashion. Previous studies have shown that other amino acid substitutions at H3-L61 result in the accumulation of Spt16 at the 3' end of transcribed genes. This study demonstrates that the H3-L61R mutant also impairs Spt16 dissociation.
Article
Multidisciplinary Sciences
Jiao Chen, Zuer Lu, Weibin Gong, Xue Xiao, Xiaoli Feng, Wei Li, Shan Shan, Dongyi Xu, Zheng Zhou
Summary: Inhibition of host DNA damage response (DDR) by viruses is a common mechanism to manipulate host cellular machinery and orchestrate viral life cycles. Here, the study reveals the structural basis of Epstein-Barr virus tegument protein BKRF4 binding to partially unfolded nucleosomes and elucidates an unconventional mechanism of host DDR signal attenuation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Wladyslaw A. Krajewski
Summary: Tight packaging of DNA in chromatin restricts DNA accessibility and dynamics, while studying the inherent dynamics and interactions of nucleosomes is crucial for understanding their functionality and diversifying epigenetic programming methods.
FRONTIERS IN GENETICS
(2022)
Article
Critical Care Medicine
Nadir Yehya, Hossein Fazelinia, Gladys G. Lawrence, Lynn A. Spruce, Mark Mai, G. Scott Worthen, Jason D. Christie
Summary: This study found that plasma nucleosomes are associated with the severity of acute respiratory distress syndrome (ARDS) in children, as well as with nonpulmonary organ failures. Nucleosomes were also linked to higher mortality rates and fewer ventilator-free days in the pediatric ARDS patients. Proteomic analysis further showed elevated levels of core nucleosome histones in septic children with ARDS.
CRITICAL CARE MEDICINE
(2021)
Article
Cell Biology
Ines Schoberleitner, Ingo Bauer, Anming Huang, Evgeniya N. Andreyeva, Johanna Sebald, Katharina Pascher, Dietmar Rieder, Melanie Brunner, Valerie Podhraski, Gregor Oemer, Daniel Cazarez-Garcia, Leila Rieder, Markus A. Keller, Robert Winkler, Dmitry Fyodorov, Alexandra Lusser
Summary: CHD1 is essential for assembling H3.3 chromatin in adult cells, particularly in the brain, playing a crucial role in regulating organismal health and longevity.
Article
Chemistry, Multidisciplinary
Wenjun Sun, Olga O. Lebedenko, Nicole Gonzalez Salguero, Matthew D. Shannon, Mohamad Zandian, Michael G. Poirier, Nikolai R. Skrynnikov, Christopher P. Jaroniec
Summary: The nucleosome, the fundamental repeat unit of chromatin, consists of DNA and a histone protein octamer. The histone tails play important roles in chromatin compaction and regulation. This study investigates the conformation and interactions of histone H4 tails in nucleosomes using experimental results and molecular dynamics simulations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Gauri Deak, Atlanta G. Cook
Summary: Missense variants are alterations to protein coding sequences that can reflect negative selection on protein structure and function. In this study, a set of tools for visualizing missense variants on protein structures was developed and applied to investigate the functional roles of ARID family gene regulators. Comparative analysis of missense depletion patterns among paralogs revealed sub-functionalization.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Cell Biology
Liat Oss-Ronen, Tzlil Sarusi, Idan Cohen
Summary: Epigenetic regulation, specifically histone mono-ubiquitination, plays a crucial role in shaping chromatin epigenetic landscape and cellular identity during tissue development and pathologies.