Article
Biochemistry & Molecular Biology
Anagh Ray, Preeti Khan, Ronita Nag Chaudhuri
Summary: The study highlights the importance of lysine acetylation in maintaining chromatin structure and function, specifically focusing on the role of H4K16 acetylation in regulating the expression of constitutive genes. Deacetylation of H4K16 is associated with hypoacetylation of H4K12 and H3K9, along with hyperacetylation of H3K56, creating a chromatin landscape conducive for transcription of constitutive genes.
Article
Biology
Calvin Jon A. Leonen, Miho Shimada, Caroline E. Weller, Tomoyoshi Nakadai, Peter L. Hsu, Elizabeth L. Tyson, Arpit Mishra, Patrick M. M. Shelton, Martin Sadilek, R. David Hawkins, Ning Zheng, Robert G. Roeder, Champak Chatterjee
Summary: Post-translational modification of histones by the small ubiquitin-like modifier protein SUMO plays a key role in gene silencing, centromeric localization, and DNA repair in eukaryotes. The study demonstrated that H4K12su inhibits acetylation of H4 tail and methylation of H3K4 associated with transcription activation, as well as transcription mediated by RNA polymerase II. Cell-based assays confirmed the negative crosstalk between histone sumoylation and acetylation/methylation in human cells.
Article
Biology
Christine E. Cucinotta, Rachel H. Dell, Keean Ca Braceros, Toshio Tsukiyama
Summary: This study found that there is robust transcription activity within the first few minutes of quiescence exit. The chromatin-remodeling enzyme RSC is already bound to genes induced upon quiescence exit. Depletion of RSC results in severe defects during quiescence exit, including a global decrease in Pol II loading and aberrant transcription initiation.
Article
Biotechnology & Applied Microbiology
Nando D. Das, Jen-Chien Chang, Chung-Chau Hon, S. Thomas Kelly, Shinsuke Ito, Marina Lizio, Bogumil Kaczkowski, Hisami Watanabe, Keisuke Katsushima, Atsushi Natsume, Haruhiko Koseki, Yutaka Kondo, Aki Minoda, Takashi Umehara
Summary: This study found that H4K5acK8ac and H3K27ac signals have some overlap in binding to the super-enhancer transcription factor BRD4 at higher levels, but they also have distinct specificities, especially in glioblastoma stem-like cell lines. Deletion of H4K5acK8ac-preferred super-enhancers associated with MYCN and NFIC resulted in a reduction in stem-like properties.
Article
Biochemistry & Molecular Biology
Fan Kou, Lei Wu, Yu Zheng, Yeran Yi, Zhenyu Ji, Ziqi Huang, Shiwei Guo, Lili Yang
Summary: This study reveals the critical role of HMGB1 in glycolysis and metastasis in LUAD, by attenuating H3K9ace and H3K27ace through physical interaction with SET and HAT1.
Article
Biochemistry & Molecular Biology
Fan Kou, Lei Wu, Yu Zheng, Yeran Yi, Zhenyu Ji, Ziqi Huang, Shiwei Guo, Lili Yang
Summary: This study found that in lung adenocarcinoma, the overexpression of HMGB1 is associated with tumor grade and poor survival. HMGB1 interacts physically with SET and HAT1 to suppress H3K9ace and H3K27ace acetylation, promoting glycolysis and metastasis.
Article
Biochemistry & Molecular Biology
Yue Wang, Yunchao Huang, Edith Cheng, Xinhua Liu, Yu Zhang, Jianguo Yang, Jordan T. F. Young, Grant W. Brown, Xiaohan Yang, Yongfeng Shang
Summary: This study reveals an unexpected role for lysine-specific demethylase 1 (LSD1) in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. The findings support the potential use of selective inhibitors of LSD1 in cancer therapy, while emphasizing the need to maintain an appropriate level of LSD1 to minimize side effects.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Review
Biochemistry & Molecular Biology
Pin Zhao, Samiullah Malik
Summary: This review describes how phosphorylation affects the transcription activity and other functions of DNA/histone modifying enzymes. Although the phosphorylated sites of these enzymes have been classified and partially explained, further research is still needed to determine their relationship with disease-associated transcriptional regulation.
CELL AND BIOSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Deimante Zukauskaite, Aida Vitkeviciene, Akvile Zlibinaite, Raminta Bausyte, Diana Ramasauskaite, Ruta Navakauskiene
Summary: The aim of this study was to analyze the changes in epigenetic modulators, histone modifications, and DNA methylation during induced human endometrial stromal cells (ESC) in vitro decidualization. The results revealed that HDAC2 and subunits of PRC2 were down-regulated while the global level of H4hyperAc and H3K27me3 increased during ESC decidualization. Specific gene promoters' histone acetylation level also increased during the induced ESC decidualization, indicating the importance of epigenetic regulation in endometrial decidualization.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2023)
Article
Obstetrics & Gynecology
Ferran Barrachina, Alberto de la Iglesia, Meritxell Jodar, Ada Soler-Ventura, Carme Mallofre, Leonardo Rodriguez-Carunchio, Afsaneh Goudarzi, Juan Manuel Corral, Josep Lluis Ballesca, Judit Castillo, Rafael Oliva
Summary: In this study, the researchers investigated the alteration of histone H4 acetylation (H4ac) in the seminiferous tubules of testicular tumour patients. They found a considerable dysregulation of H4ac in the unaffected cells of the seminiferous tubules adjacent to the tumours, suggesting a potential paracrine effect of the neoplasia. This epigenetic alteration could have implications for the molecular changes in male germ cells in testicular tumour patients.
HUMAN REPRODUCTION
(2022)
Article
Plant Sciences
Xiaoyun Xin, Tongbing Su, Peirong Li, Weihong Wang, Xiuyun Zhao, Yangjun Yu, Deshuang Zhang, Shuancang Yu, Fenglan Zhang
Summary: The study demonstrated that BrHIS4.A04 interacts with BrVIN3.1 to prevent premature bolting by attenuating the expression of photoperiodic flowering genes through the ABA signaling pathway under drought conditions. The findings suggest the potential for fine-tuning flowering time in crops through genetic engineering without growth penalty.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Oncology
Xiaohui Pan, Wenxin Zhang, Longsheng Wang, Hongjie Guo, Mingming Zheng, Honghai Wu, Qinjie Weng, Qiaojun He, Ling Ding, Bo Yang
Summary: Recent studies have shown that Krupple-like factor 12 (KLF12) plays a crucial role in cancer-associated processes in non-small cell lung cancer (NSCLC), including proliferation, apoptosis, and metastasis. KLF12 is positively correlated with programmed death-ligand 1 (PD-L1) expression and can bind to the CACCC motif of the PD-L1 promoter to promote transcription. Knockout of KLF12 inhibits tumor growth and enhances infiltration of CD8(+) T cells in immunocompetent mice.
MOLECULAR ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Mark Boltengagen, Anke Samel-Pommerencke, David Fechtig, Ann E. Ehrenhofer-Murray
Summary: The acetylation of H4 lysine 16 in yeast regulates gene silencing by inhibiting the binding of heterochromatin complex SIR to chromatin. The SAS-I complex is a major provider of H4 K16Ac in yeast, and its absence leads to improper gene silencing. Replication disrupts histone marks, with H4 K16Ac appearing immediately and being influenced by transcription levels. Additionally, the acetyltransferases Esa1 and Sas2 redundantly regulate H4 K16Ac levels in yeast cells.
Article
Multidisciplinary Sciences
Filippo Ciabrelli, Leily Rabbani, Francesco Cardamone, Fides Zenk, Eva Loeser, Melanie A. Schaechtle, Marina Mazina, Vincent Loubiere, Nicola Iovino
Summary: We conducted an in vivo RNA interference reverse genetic screen in Drosophila melanogaster and identified histone acetyltransferases (HATs) and histone deacetylases as key regulators of zygotic genome activation (ZGA). We showed that Nejire and Gcn5 are responsible for acetylation of different lysine sites on histone H3 during ZGA, with these marks being enriched at actively transcribed genes. Surprisingly, catalytic dead mutants of Nejire or Gcn5 can still activate ZGA and transactivate a reporter gene in vitro. Overall, our study identifies Nejire and Gcn5 as crucial regulators of ZGA.
Article
Plant Sciences
Huaijian Xu, Meng Ye, Aliang Xia, Hang Jiang, Panpan Huang, Huiquan Liu, Rui Hou, Qinhu Wang, Dongao Li, Jin-Rong Xu, Cong Jiang
Summary: Fng3 is a protein that interacts with histone modification complexes, involved in the regulation of histone acetylation, and crucial for fungal development and pathogenicity.
Article
Cardiac & Cardiovascular Systems
Victoria N. Parikh, Colleen Caleshu, Chloe Reuter, Laura C. Lazzeroni, Jodie Ingles, John Garcia, Kristen McCaleb, Tolulope Adesiyun, Farbod Sedaghat-Hamedani, Saurabh Kumar, Sharon Graw, Marta Gigli, Davide Stolfo, Matteo Dal Ferro, Alexander Y. Ing, Robert Nussbaum, Birgit Funke, Matthew T. Wheeler, Ray E. Hershberger, Stuart Cook, Lars M. Steinmetz, Neal K. Lakdawala, Matthew R. G. Taylor, Luisa Mestroni, Marco Merlo, Gianfranco Sinagra, Christopher Semsarian, Benjamin Meder, Daniel P. Judge, Euan Ashley
CIRCULATION-HEART FAILURE
(2019)
Article
Multidisciplinary Sciences
Erwei Zuo, Yidi Sun, Wu Wei, Tanglong Yuan, Wenqin Ying, Hao Sun, Liyun Yuan, Lars M. Steinmetz, Yixue Li, Hui Yang
Article
Biochemistry & Molecular Biology
Sivan Kaminski Strauss, Dvir Schirman, Ghil Jona, Aaron N. Brooks, Aditya M. Kunjapur, Alex N. Nguyen Ba, Alice Flint, Andras Solt, Andreas Mershin, Atray Dixit, Avihu H. Yona, Balint Csorgo, Bede Phillip Busby, Bianca P. Hennig, Csaba Pal, Daniel Schraivogel, Daniel Schultz, David G. Wernick, Deepa Agashe, Dikla Levi, Dmitry Zabezhinsky, Dor Russ, Ehud Sass, Einat Tamar, Elad Herz, Emmanuel D. Levy, George M. Church, Idan Yelin, Iftach Nachman, Jeffrey E. Gerst, Joseph M. Georgeson, Katarzyna P. Adamala, Lars M. Steinmetz, Marc Ruebsam, Markus Ralser, Michael Klutstein, Michael M. Desai, Nilima Walunjkar, Ning Yin, Noa Aharon Hefetz, Noah Jakimo, Olga Snitser, Omri Adini, Prashant Kumar, Rachel Soo Hoo Smith, Razi Zeidan, Ronen Hazan, Roni Rak, Roy Kishony, Shannon Johnson, Shira Nouriel, Sibylle C. Vonesch, Simmie Foster, Tal Dagan, Tanita Wein, Thrasyvoulos Karydis, Timothy M. Wannier, Timothy Stiles, Viridiana Olin-Sandoval, William F. Mueller, Yinon M. Bar-On, Orna Dahan, Yitzhak Pilpel
Article
Multidisciplinary Sciences
Naresha Saligrama, Fan Zhao, Michael J. Sikora, William S. Serratelli, Ricardo A. Fernandes, David M. Louis, Winnie Yao, Xuhuai Ji, Juliana Idoyaga, Vinit B. Mahajan, Lars M. Steinmetz, Yueh-Hsiu Chien, Stephen L. Hauser, Jorge R. Oksenberg, K. Christopher Garcia, Mark M. Davis
Article
Biochemistry & Molecular Biology
Haruhiko Fujihira, Yuki Masahara-Negishi, Yoshihiro Akimoto, Hiroto Hirayama, Hyeon-Cheol Lee, Benjamin A. Story, William F. Mueller, Petra Jakob, Sandra Clauder-Muenster, Lars M. Steinmetz, Senthil K. Radhakrishnan, Hayato Kawakami, Yoshihiro Kamada, Eiji Miyoshi, Takehiko Yokomizo, Tadashi Suzuki
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2020)
Article
Cell Biology
Chiara Baccin, Jude Al-Sabah, Lars Velten, Patrick M. Helbling, Florian Gruenschlaeger, Pablo Hernandez-Malmierca, Cesar Nombela-Arrieta, Lars M. Steinmetz, Andreas Trumpp, Simon Haas
NATURE CELL BIOLOGY
(2020)
Article
Biochemical Research Methods
Daniel Schraivogel, Andreas R. Gschwind, Jennifer H. Milbank, Daniel R. Leonce, Petra Jakob, Lukas Mathur, Jan O. Korbel, Christoph A. Merten, Lars Velten, Lars M. Steinmetz
Article
Genetics & Heredity
William F. Mueller, Petra Jakob, Han Sun, Sandra Clauder-Muenster, Sonja Ghidelli-Disse, Diana Ordonez, Markus Boesche, Marcus Bantscheff, Paul Collier, Bettina Haase, Vladimir Benes, Malte Paulsen, Peter Sehr, Joe Lewis, Gerard Drewes, Lars M. Steinmetz
G3-GENES GENOMES GENETICS
(2020)
Article
Biochemical Research Methods
Erwei Zuo, Yidi Sun, Wu Wei, Tanglong Yuan, Wenqin Ying, Hao Sun, Liyun Yuan, Lars M. Steinmetz, Yixue Li, Hui Yang
Article
Biochemistry & Molecular Biology
Jingwen Wang, Bingnan Li, Sueli Marques, Lars M. Steinmetz, Wu Wei, Vicent Pelechano
NUCLEIC ACIDS RESEARCH
(2020)
Article
Cell Biology
Francesca Briganti, Han Sun, Wu Wei, Jingyan Wu, Chenchen Zhu, Martin Liss, Ioannis Karakikes, Shannon Rego, Andrea Cipriano, Michael Snyder, Benjamin Meder, Zhenyu Xu, Gilles Millat, Michael Gotthardt, Mark Mercola, Lars M. Steinmetz
Article
Biology
Kristen L. Wells, Corey N. Miller, Andreas R. Gschwind, Wu Wei, Jonah D. Phipps, Mark S. Andersonz, Lars M. Steinmetz
Article
Genetics & Heredity
Sibylle C. Vonesch, Shengdi Li, Chelsea Szu Tu, Bianca P. Hennig, Nikolay Dobrev, Lars M. Steinmetz
Summary: The study presents a highly scalable method for preparing high-quality whole-genome sequencing libraries directly from Saccharomyces cerevisiae cultures in less than 3 hours at 34 cents per sample. By skipping the step of genomic DNA extraction, adding a nucleosome release step, and enriching PCR, the resulting libraries show even genomic coverage and quality comparable to commercially available kits. This protocol enables rapid preparation of unbiased and high-quality sequencing libraries for hundreds of yeast strains in a single day at a low price.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Jay W. Schneider, Saji Oommen, Muhammad Y. Qureshi, Sean C. Goetsch, David R. Pease, Rhianna S. Sundsbak, Wei Guo, Mingming Sun, Han Sun, Hidehito Kuroyanagi, Dennis A. Webster, Alexander W. Coutts, Kimberly A. Holst, Brooks S. Edwards, Nikolas Newville, Matthew A. Hathcock, Tamene Melkamu, Francesca Briganti, Wu Wei, Maria G. Romanelli, Scott C. Fahrenkrug, Doug E. Frantz, Timothy M. Olson, Lars M. Steinmetz, Daniel F. Carlson, Timothy J. Nelson
Article
Materials Science, Biomaterials
Semih Calamak, Menekse Ermis, Han Sun, Saiful Islam, Michael Sikora, Michelle Nguyen, Vasif Hasirci, Lars M. Steinmetz, Utkan Demirci
ADVANCED BIOSYSTEMS
(2020)