Article
Medicine, Research & Experimental
Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret A. Gruca, Jonathan H. Cardwell, Tsukasa Okamoto, Hong W. Chu, Xiaomeng Hou, Olivier B. Poirion, Justin Buchanan, Sebastian Preissl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana Yang, David A. Schwartz, Anthony N. Gerber
Summary: The G/T transversion rs35705950, located 3 kb upstream of the MUC5B start site, is identified as a key risk factor for idiopathic pulmonary fibrosis. Through analysis of accessible chromatin and nuclease sensitivity data, it is shown that this region affects the expression of MUC5B and is subject to epigenetic remodeling in IPF patients' lung tissue.
Article
Cell & Tissue Engineering
Jiayi Chen, Guangqin Liu, Xinzheng Wang, Hao Hong, Tingting Li, Lin Li, Hongxiang Wang, Jiong Xie, Bohan Li, Ting Li, Dingyi Lu, Yakun Zhang, Haixin Zhao, Chengcheng Yao, Kaiqing Wen, Teng Li, Jing Chen, Shengming Wu, Kun He, Wei-Na Zhang, Jie Zhao, Na Wang, Qiuying Han, Qing Xia, Ji Qi, Juxiang Chen, Tao Zhou, Jianghong Man, Xue-Min Zhang, Ai-Ling Li, Xin Pan
Summary: This study explores the communication between glioblastoma stem cells (GSCs) and the microenvironment, revealing that GSCs secrete histamine to shape a pro-angiogenic tumor microenvironment. The secretion of histamine by GSCs is associated with the expression and modification of the HDC gene, and the histamine activates endothelial cells through the H1R-Ca2+-NF-kB axis, promoting angiogenesis and GBM progression. The findings suggest that targeting histamine could be a potential strategy for GBM therapy.
Article
Cell Biology
Jasmine Li, Kristine Hardy, Moshe Olshansky, Adele Barugahare, Linden J. Gearing, Julia E. Prier, Xavier Y. X. Sng, Michelle Ly Thai Nguyen, Dana Piovesan, Brendan E. Russ, Nicole L. La Gruta, Paul J. Hertzog, Sudha Rao, Stephen J. Turner
Summary: New research has revealed that rapid upregulation of the histone demethylase KDM6B is crucial for initiating H3K27me3 removal and promoting T cell differentiation and proliferation after CD8(+) T cell activation. Inhibiting KDM6B-dependent H3K27me3 demethylation limits the effectiveness of primary virus-specific CD8(+) T cell response and the formation of memory CD8(+) T cell populations. The study defines early spatial and temporal events necessary for chromatin reprogramming in CD8(+) T cells for autonomous proliferation and differentiation.
Article
Neurosciences
Ines Schoberleitner, Birte Mertens, Ingo Bauer, Alexandra Lusser
Summary: The ATP-dependent chromatin remodeling factor CHD1 plays a crucial role in the incorporation of the histone variant H3.3 in the fly brain, affecting sensory perception genes and leading to defects in olfactory and gustatory response behavior. Additionally, Chd1-mutant flies exhibit shortened lifespan and indications of premature functional aging, including impaired negative geotaxis and exploratory walking. Neuronal re-expression of Chd1 rescues the exploratory walking phenotype but not the olfactory defects.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Celine Duc, Christophe Thiriet
Summary: The review focuses on the remodeling of chromatin during DNA replication in the S-phase, including the eviction of nucleosomes and the assembly of newly synthesized histones. The recycling of parental histones and the nuclear import of histones are also discussed in relation to epigenetic inheritance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Ji-Yun Shang, Xin-Jian He
Summary: Adenosine triphosphate-dependent chromatin remodeling complexes play a crucial role in transcription, DNA replication, and genome stability regulation in eukaryotes. However, the study of chromatin remodeling complexes in plants lags behind yeast and animals. Recent research has identified and characterized the composition and function of chromatin remodeling enzymes in Arabidopsis, providing a foundation for further investigation into the molecular mechanisms.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lihua Wang, Ergang Wang, Jorge Prado Balcazar, Zhenzhen Wu, Kun Xiang, Yi Wang, Qiang Huang, Marcos Negrete, Kai-Yuan Chen, Wei Li, Yujie Fu, Anders Dohlman, Robert Mines, Liwen Zhang, Yoshihiko Kobayashi, Tianyi Chen, Guizhi Shi, John Paul Shen, Scott Kopetz, Purushothama Rao Tata, Victor Moreno, Charles Gersbach, Gregory Crawford, David Hsu, Emina Huang, Pengcheng Bu, Xiling Shen
Summary: Metastatic colorectal cancer cells undergo specific chromatin remodeling in the liver, facilitated by hepatic growth factor-induced phosphorylation of PU.1. This epigenetic modification allows for the growth of tumor cells in their new niche and could potentially be targeted for therapeutic intervention. Individual genetic silencing or pharmacological inhibition along this chromatin remodeling axis can strongly suppress liver metastasis.
Article
Biochemical Research Methods
Dan Huang, Xiansong Wang, Yingzhi Liu, Ziheng Huang, Xiaoxu Hu, Wei Hu, Qing Li, Hung Chan, Yidan Zou, Idy H. T. Ho, Yan Wang, Alfred S. L. Cheng, Wei Kang, Ka F. To, Maggie H. T. Wang, Sunny H. Wong, Jun Yu, Tony Gin, Qingpeng Zhang, Zheng Li, Jianxiong Shen, Lin Zhang, Matthew T. Chan, Xiaodong Liu, William K. K. Wu
Summary: Tumor suppressor genes exhibit unique promoter features that optimize cancer resistance by achieving high expression in normal tissues and resisting downregulation during tumorigenesis. The CpG dinucleotide frequencies in TSG promoters are higher and positively correlated with gene expression, suggesting an evolutionary pressure on young TSGs. Higher CpG frequencies and chromatin accessibility are associated with the ability of TSGs to resist downregulation during tumorigenesis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Yushun Zhang, Qiong Chen, Guanlin Zhu, Dechun Zhang, Weihong Liang
Summary: In this study, it was found that the C-terminal of the chromatin-remodeling factor CHR721 with a non-canonical PIP-box is essential for interacting with OsPCNA in rice, indicating that CHR721 and OsPCNA may play a critical role in DNA damage repair.
Article
Biochemistry & Molecular Biology
Farshad Niri, Alaina N. Terpstra, Kenji Rowel Q. Lim, Heather E. McDermid
Summary: CECR2 is a chromatin remodeling factor crucial for neural tube closure and reproduction. Loss-of-function mutations in Cecr2 primarily result in perinatal lethal neural tube defect exencephaly, with non-penetrant mice showing subfertility. The CECR2-containing remodeling factor (CERF) complex in embryonic stem cells includes SMARCA5, SMARCA1, CCAR2, and LUZP1, with LUZP1 potentially playing a role in stabilizing the complex in ES cells.
BIOCHEMISTRY AND CELL BIOLOGY
(2021)
Article
Genetics & Heredity
R. D. Acemel, J. J. Tena, J. L. Gomez-Skarmeta, J. Fibla, J. L. Royo
Summary: A key advance in understanding gene regulation is the discovery of three-dimensional nuclear folding in the genome, influencing enhancer-promoter interactions. New technologies quantifying these DNA interactions have revolutionized the field, but may lack resolution for subtle effects of single nucleotide polymorphisms. The impact of a common deletion between the SIRPB1 promoter and one of its downstream enhancers was analyzed as proof of concept for a cost-efficient allele-specific chromatin conformation analysis approach.
Article
Biophysics
Shalini Pradhan, Sinem Apaydin, Jonas Bucevicius, Ruta Gerasimaite, Georgij Kostiuk, Grazvydas Lukinavicius
Summary: In this review, we summarize various sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatments and DNA denaturation. These methods include hairpin polyamides, triplex-forming oligonucleotides, dCas9 proteins, transcription activator-like effectors (TALEs), and DNA methyltransferases (MTases). The goal is to eventually replace the traditionally used fluorescence in situ hybridization (FISH) with less invasive and non-destructive methods that are compatible with live cell imaging, allowing for the examination of chromatin structure and dynamics in living cells, tissues, and organisms.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Plant Sciences
Yin-Ai Deng, Li Li, Qian Peng, Ling-Fang Feng, Jin-Fen Yang, Ruo-Ting Zhan, Dong-Ming Ma
Summary: In this study, a C2H2-type transcription factor AaZFP1 was found to bind to the AGT-N1-10-AGT box of AaIPPI1pro and activate the expression of AaIPPI1 involved in artemisinin biosynthesis. This provides insights into the transcriptional regulation of genes involved in artemisinin biosynthesis in Artemisia annua.
Article
Immunology
Ana C. F. Ferreira, Aydan C. H. Szeto, Paula A. Clark, Alastair Crisp, Patrycja Kozik, Helen E. Jolin, Andrew N. J. McKenzie
Summary: The study found that ADNP plays an indispensable role in immune reactions to allergens by recruiting proteins such as CHD4 and BRG1, serving as a critical bridge in gene activation and promoting T cell differentiation. The absence of ADNP impairs the ability of GATA3 and AP-1 to initiate histone acetylation and DNA accessibility, resulting in impaired expression of type 2 cytokines. These results demonstrate the importance of ADNP in promoting immune cell specialization.
Article
Biochemistry & Molecular Biology
Roberto Amigo, Carlos Farkas, Cristian Gidi, Matias Hepp, Natalia Cartes, Estefania Tarifeno, Jerry L. Workman, Jose L. Gutierrez
Summary: This study compares the properties and interactions of Hmo1 and Hho1 proteins, and finds that Hmo1 belongs to the HMGB family while Hho1 belongs to the linker histones family. In addition, Hmo1 and Hho1 display differential effects on chromatin remodeling complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Review
Biochemistry & Molecular Biology
Andreas Hasso Ehrensberger, Jesper Qualmann Svejstrup
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Yuichiro Takagi, Guillermo Calero, Hirofumi Komori, Jesse A. Brown, Andreas H. Ehrensberger, Andy Hudmon, Francisco Asturias, Roger D. Kornberg
Article
Biochemistry & Molecular Biology
AH Ehrensberger, RA Elling, DK Wilson
Article
Biochemistry & Molecular Biology
AH Ehrensberger, DK Wilson
JOURNAL OF MOLECULAR BIOLOGY
(2004)