Review
Biochemistry & Molecular Biology
Hirotomo Takatsuka, Atsushi Shibata, Masaaki Umeda
Summary: Plant DNA is vulnerable to environmental stressors, and chromatin plays a crucial role in protecting DNA by altering its structure. Changes in chromatin modifications, regulation of gene expression, and the physical barrier function of condensed chromatin are key mechanisms for plants to maintain genome integrity under genotoxic stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Karolina Kolarova, Martina Nespor Dadejova, Tomas Loja, Gabriela Lochmanova, Eva Sykorova, Martina Dvorackova
Summary: The disruption of the H2A-H2B histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) can suppress the loss-of-function phenotype of FAS1, leading to wild-type growth, decreased sensitivity to genotoxic stress, and suppression of telomere and 45S rDNA loss in Arabidopsis thaliana. This study demonstrates the essential role of NAP1 proteins in DNA repair in the absence of functional CAF-1, which is coupled to nucleosome assembly through modulation of H3 levels in the nucleus.
Article
Multidisciplinary Sciences
Osama Garwain, Xiaoming Sun, Divya Ramalingam Iyer, Rui Li, Lihua Julie Zhu, Paul D. Kaufman
Summary: The depletion of Ki-67 in vertebrate mammals can cause DNA damage, particularly in mitotic cells. The C-terminal chromatin-binding domain of Ki-67 plays a crucial role in protecting cells from this damage. Simultaneous depletion of Ki-67 and p53 results in increased chromosome bridges and micronuclei, highlighting the importance of Ki-67 in maintaining genome stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Uma P. Arora, Beth A. Sullivan, Beth L. Dumont
Summary: This study investigates the interplay between centromere variation and kinetochore protein sequence association in mice, and reveals strain-level differences in both CENP-A positioning and sequence preference along the core centromere satellite.
Article
Biochemistry & Molecular Biology
Claudia Moriello, Martina Costabile, Michele Spinelli, Angela Amoresano, Giancarlo Palumbo, Ferdinando Febbraio, Marina Piscopo
Summary: In this study, the effect of Cr(VI) exposure on the reproductive health of Mytilus galloprovincialis was evaluated. It was found that exposure to 1 nM Cr(VI) resulted in reduced binding and protective abilities of Protamine-like proteins and alterations in gene expression.
Review
Cell Biology
Lishu He, Gwen Lomberk
Summary: Disrupted DNA damage signaling poses a significant threat to cell integrity and is closely associated with cancer development. Recent advances in chromatin biology, particularly in histone post-translational modifications, have shown great promise for cancer therapeutics. Key histone methylation pathways play a crucial role in DNA damage repair and tumorigenesis, making them potential targets for cancer treatment strategies.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Juliette Ferrand, Alexandre Plessier, Sophie E. Polo
Summary: DNA damage leads to changes in histone protein dynamics and modifications, impacting the stability of the epigenome. However, these alterations also play a crucial role in facilitating an efficient response to DNA damage.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Benjamin T. Donovan, Yi Luo, Zhiyuan Meng, Michael G. Poirier
Summary: Transcription factors (TF) need access to target sites within nucleosomes to initiate transcription. The position of the target site within the nucleosome significantly affects TF occupancy, but the quantitative mechanism is not fully understood. Through fluorescence measurements, we studied the targeting and occupancy of the transcription factor Gal4 at different positions within the nucleosome. We found that the nucleosome unwrapping free energy landscape is the primary determinant of Gal4 occupancy by reducing the Gal4 binding rate.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Linda C. Horianopoulos, Christopher W. J. Lee, Kerstin Schmitt, Oliver Valerius, Guanggan Hu, Melissa Caza, Gerhard H. Braus, James W. Kronstad
Summary: This study identifies a nuclear J domain protein, Dnj4, in the fungal pathogen Cryptococcus neoformans, demonstrating its role as a histone chaperone important for maintaining genome integrity and responding to DNA damage. Dnj4 regulates iron homeostasis and plays a crucial role in DNA damage response in C. neoformans. Additionally, Dnj4 functions as a conserved histone chaperone disrupting endogenous histone chaperoning machinery, suggesting its potential in understanding biological processes across different organisms.
Review
Cell Biology
Wentao Li, Kyle Jones, Tyler J. Burke, Md Akram Hossain, Leah Lariscy
Summary: Genomic DNA is constantly exposed to various DNA damaging agents, and nucleotide excision repair (NER) is a versatile pathway that can remove bulky and helix-distorting DNA lesions. The NER process is more complex inside cells due to the tight packaging of genomic DNA into chromosomes and the compaction into the nucleus. Additionally, epigenetic modifications play a crucial role in regulating gene activity and expression during the in vivo NER process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
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
Multidisciplinary Sciences
Jiangbin Wei, Qiwu Shi, Lidan Xiong, Guang Xin, Tao Yi, Yunqing Xiao, Wanxia Huang
Summary: The study investigated the biological effects of radiation from the SG-III prototype laser facility on HaCat cells and PC12 cells, finding that the damage to cells was dose-dependent and induced DNA damage and apoptotic necrosis. Transcriptome and protein analysis revealed pathways involving proliferation, transformation, necrosis, inflammation response, apoptosis, and DNA damage repair were activated, suggesting potential harm to biological safety.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Ren Yi, Kyunghyun Cho, Richard Bonneau
Summary: In this paper, we propose NetTIME, a multitask learning framework for predicting cell-type-specific TF binding sites. The multitask learning strategy is shown to be more efficient than single-task approach due to increased data availability. By training high-dimensional embedding vectors to distinguish TF and cell-type identities, our model achieves accurate transfer predictions within and beyond the training panels. Additionally, a linear-chain conditional random field (CRF) is trained to classify binding predictions, eliminating the need for a probability threshold and reducing classification noise. Our method outperforms previous methods, Catchitt and Leopard, in both supervised and transfer learning settings.
Article
Biochemical Research Methods
Margaret E. Wilson, Shin-Cheng Tzeng, Megan M. Augustin, Matthew Meyer, Xiaoyue Jiang, Jae H. Choi, John C. Rogers, Bradley S. Evans, Toni M. Kutchan, Dmitri A. Nusinow
Summary: Protein phosphorylation is a crucial posttranslational modification in eukaryotic systems, and MLKs play a key role in regulating protein dynamics and plant metabolism, connecting environmental stimuli to developmental processes.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Review
Plant Sciences
Valentin Joly, Yannick Jacob
Summary: This study summarizes recent discoveries in plants regarding the role of H3.1 in chromatin replication, genomic stability, epigenetic inheritance, and its interaction with DNA polymerase epsilon.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Kaycie C. Hopkins, Michael A. Tartell, Christin Herrmann, Brent A. Hackett, Frances Taschuk, Debasis Panda, Sanjay V. Menghani, Leah R. Sabin, Sara Cherry
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Multidisciplinary Sciences
Xaver Sewald, Mark S. Ladinsky, Pradeep D. Uchil, Jagadish Beloor, Ruoxi Pi, Christin Herrmann, Nasim Motamedi, Thomas T. Murooka, Michael A. Brehm, Dale L. Greiner, Leonard D. Shultz, Thorsten R. Mempel, Pamela J. Bjorkman, Priti Kumar, Walther Mothes
Article
Multidisciplinary Sciences
Daphne C. Avgousti, Christin Herrmann, Katarzyna Kulej, Neha J. Pancholi, Nikolina Sekulic, Joana Petrescu, Rosalynn C. Molden, Daniel Blumenthal, Andrew J. Paris, Emigdio D. Reyes, Philomena Ostapchuk, Patrick Hearing, Steven H. Seeholzer, G. Scott Worthen, Ben E. Black, Benjamin A. Garcia, Matthew D. Weitzman
Article
Biochemical Research Methods
Katarzyna Kulej, Daphne C. Avgousti, Simone Sidoli, Christin Herrmann, Ashley N. Della Fera, Eui Tae Kim, Benjamin A. Garcia, Matthew D. Weitzman
MOLECULAR & CELLULAR PROTEOMICS
(2017)
Article
Virology
Fei Li, Jing Jin, Christin Herrmann, Walther Mothes
JOURNAL OF VIROLOGY
(2013)
Article
Multidisciplinary Sciences
Susanne L. Linderman, Benjamin S. Chambers, Seth J. Zost, Kaela Parkhouse, Yang Li, Christin Herrmann, Ali H. Ellebedy, Donald M. Carter, Sarah F. Andrews, Nai-Ying Zheng, Min Huang, Yunping Huang, Donna Strauss, Beth H. Shaz, Richard L. Hodinka, Gustavo Reyes-Teran, Ted M. Ross, Patrick C. Wilson, Rafi Ahmed, Jesse D. Bloom, Scott E. Hensley
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Virology
Joseph M. Dybas, Christin Herrmann, Matthew D. Weitzman
CURRENT OPINION IN VIROLOGY
(2018)
Review
Biochemistry & Molecular Biology
Matthew Charman, Christin Herrmann, Matthew D. Weitzman
Article
Cell Biology
Joel D. Federspiel, Katelyn C. Cook, Michelle A. Kennedy, Samvida S. Venkatesh, Clayton J. Otter, William A. Hofstadter, Pierre M. Jean Beltran, Ileana M. Cristea
Article
Microbiology
Christin Herrmann, Joseph M. Dybas, Jennifer C. Liddle, Alexander M. Price, Katharina E. Hayer, Richard Lauman, Caitlin E. Purman, Matthew Charman, Eui Tae Kim, Benjamin A. Garcia, Matthew D. Weitzman
NATURE MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Cora N. Betsinger, Connor S. R. Jankowski, William A. Hofstadter, Joel D. Federspiel, Clayton J. Otter, Pierre M. Jean Beltran, Ileana M. Cristea
Summary: The study reveals how the prevalent pathogen HCMV increases mitochondrial metabolism and cellular respiration through the viral protein pUL13, promoting virus replication. Interaction of pUL13 with the MICOS complex alters mitochondrial structure and affects oxidative phosphorylation process in cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Courtney E. Comar, Clayton J. Otter, Jessica Pfannenstiel, Ethan Doerger, David M. Renner, Li Hui Tan, Stanley Perlman, Noam A. Cohen, Anthony R. Fehr, Susan R. Weiss
Summary: MERS-CoV optimizes its replication by suppressing early innate immune pathways, including interferon production and signaling, through the actions of endoribonuclease (EndoU) and accessory proteins NS4a and NS4b.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)