Review
Biochemistry & Molecular Biology
Emilia J. Orzechowska-Licari, Joseph F. LaComb, Aisharja Mojumdar, Agnieszka B. Bialkowska
Summary: Tumor development and progression rely on the reprogramming of signaling pathways that regulate cell metabolism, with transcription factors SP and KLF playing crucial roles in modulating these alterations and thus impacting tumorigenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ralph S. Grand, Lukas Burger, Cathrin Grawe, Alicia K. Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, Vytautas Iesmantavicius, Sevi Durdu, Marco Pregnolato, Arnaud R. Krebs, Sebastien A. Smallwood, Nicolas Thoma, Michiel Vermeulen, Dirk Schubeler
Summary: The study reveals that BANP is a critical transcription activator that binds to the CGCG element, controlling essential metabolic genes in pluripotent stem cells and neuronal cells. BANP binding is influenced by DNA methylation, restricting most binding to CGIs and explaining differential binding at CGI promoters in cancer cells. Additionally, BANP's binding to unmethylated motifs leads to chromatin opening and nucleosome phasing.
Article
Plant Sciences
Junhui Zhou, John Sittmann, Lei Guo, Yuwei Xiao, Xiaolong Huang, Anuhya Pulapaka, Zhongchi Liu
Summary: By studying the wild strawberry mutants in GA and auxin signaling during early fruit development, it was found that FveRGA1 is a key regulator of fruit set, while FveARF8 and FveGID1c play important roles in auxin and GA signaling pathways. The work revealed a crosstalk mechanism between FveARF8 in auxin signaling and FveGID1c in GA signaling, providing insights into hormone signaling in strawberry fruit development.
Article
Plant Sciences
Zeeshan Nasim, Hendry Susila, Suhyun Jin, Geummin Youn, Ji Hoon Ahn
Summary: The RNA polymerase II-associated factor 1 complex (PAF1C) regulates temperature-responsive flowering by modulating the transcription of FLC and FLC-clade genes, playing an important role in enhancing plant cold tolerance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Lijing Bu, Richard M. Cripps
Summary: By analyzing 330 known MEF2 target promoters in Drosophila, we found that these promoters contain specific consensus sequences associated with transcriptional activation. One prominent sequence, NDM2, was found to be over-expressed in MEF2 target genes. However, mutating the NDM2 site did not affect the activity of these promoters.
Article
Multidisciplinary Sciences
Yanfeng He, Shigeo Sato, Chieri Tomomori-Sato, Shiyuan Chen, Zach H. Goode, Joan W. Conaway, Ronald C. Conaway
Summary: The bZIP transcription factor ATF6 alpha is a master regulator of ER stress response genes, with the multifunctional RNA polymerase II transcription factor Elongin identified as a cofactor for ATF6 alpha-dependent transcription activation. Studies show that Elongin facilitates ATF6 alpha-dependent loading of Mediator at the promoters and enhancers of ER stress response genes, and depletion of Elongin leads to impaired transcription and recruitment of Mediator and its CDK8 kinase subunit during the ER stress response. Overall, these findings reveal a crucial role for Elongin as a loading factor for Mediator in the context of ER stress response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Duy T. Nguyen, Wei Yang, Arun Renganathan, Cody Weimholt, Duminduni H. Angappulige, Thanh Nguyen, Robert W. Sprung, Gerald L. Andriole, Eric H. Kim, Nupam P. Mahajan, Kiran Mahajan
Summary: This study reveals that HOXB13 exacerbates the antagonism of androgen receptor (AR) in castration-resistant prostate cancers (CRPC), and identifies a novel lysine 13 (K13) acetylation in HOXB13. Acetylated K13-HOXB13 serves as a clinical biomarker for the development of CRPC and promotes the expression of lineage, diagnostic, CRPC-promoting, and angiogenesis genes. The HOXB13 target ACK1 could be a potential therapeutic target for inhibiting CRPC growth.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
Tianyu Zheng, Jinrong Huang, Xi Xiang, Siyuan Li, Jiaying Yu, Kunli Qu, Zhe Xu, Peng Han, Zhanying Dong, Yang Liu, Fengping Xu, Huanming Yang, Marja Jaeaettelae, Yonglun Luo, Bin Liu
Summary: CREB1 is a transcription factor that responds to cAMP levels and controls the expression of target genes, regulating nutrition partitioning. While it plays an essential role in promoting tumor development, the full gene network constitutively regulated by CREB1 in tumors remains unrevealed. However, the known genes constitutively regulated by CREB1 in tumors are implicated in promoting tumorigenesis.
CANCER CELL INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Nisha Misra, Manohar Damara, Pierre Chambon
Summary: This article investigates the role of transcriptional regulators RevErbα, E4BP4, and CRY1/PER1 in generating circadian rhythms. Molecular and genetic analyses reveal that the chromatin protein HP1α plays a crucial role in transcriptional repressions of circadian clock genes and their output genes. The presence of HP1α is critical for chromatin compaction, formation of repressed biomolecular hydrophobic condensates, and recruitment and methylation of DNA methylating enzymes on the intronic deoxyCpG islands within the circadian output genes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Eva C. Henningsen, Vahid Omidvar, Rafael Della Coletta, Jean-Michel Michno, Erin Gilbert, Feng Li, Marisa E. Miller, Chad L. Myers, Sean P. Gordon, John P. Vogel, Brian J. Steffenson, Shahryar F. Kianian, Cory D. Hirsch, Melania Figueroa
Summary: Studies on gene expression changes in wheat infected by Pgt have identified processes related to susceptibility. By analyzing gene expression in wheat and Brachypodium, potential strategies to enhance resistance to Pgt have been proposed.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Liuying Gao, Hao Rong
Summary: This study investigates the potential mechanism of eRNAs in stomach adenocarcinoma, identifies tumor-related genes, constructs a highly accurate prognostic prediction model, and explores the differences between high-risk and low-risk groups using multi-omics data.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Kyle Delaney, Minjia Tan, Zhesi Zhu, Jinjun Gao, Lunzhi Dai, Sunjoo Kim, Jun Ding, Maomao He, Levon Halabelian, Lu Yang, Prabakaran Nagarajan, Mark Robert Parthun, Sangkyu Lee, Saadi Khochbin, Yujun George Zheng, Yingming Zhao
Summary: Histone lysine methacrylation (Kmea) is a newly discovered type of histone posttranslational modification, confirmed through diverse chemical approaches and identification of 27 modified histone sites. The modification is shown to be a dynamic mark controlled by HAT1 as a methacryltransferase and SIRT2 as a de-methacrylase, suggesting its involvement in epigenome-associated metabolic pathways.
Article
Biochemistry & Molecular Biology
Heng Deng, Yao Chen, Ziyu Liu, Zhaoqiao Liu, Peng Shu, Ruochen Wang, Yanwei Hao, Dan Su, Julien Pirrello, Yongsheng Liu, Zhengguo Li, Don Grierson, James J. Giovannoni, Mondher Bouzayen, Mingchun Liu
Summary: This study reveals that SlERF.F12, an ethylene response factor, negatively regulates the initiation of tomato fruit ripening by recruiting a co-repressor and histone deacetylases. SlERF.F12 interacts with the co-repressor and recruits histone deacetylases to form a complex, which decreases the acetylation level at the promoter regions of ripening genes, thus repressing their transcription.
Article
Veterinary Sciences
Jianfang Wang, Bingzhi Li, Xinran Yang, Chengcheng Liang, Sayed Haidar Abbas Raza, Yueting Pan, Ke Zhang, Linsen Zan
Summary: In this study, RNA-seq and ATAC-seq techniques were used to identify differentially expressed genes specifically expressed in bovine skeletal muscle. The results revealed key regulatory genes that are involved in skeletal muscle development. Motif analysis further identified potential target genes of the transcription factor MEF2C.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Pathology
Saran Lotfollahzadeh, Dominic Lo, Emily A. York, Marc A. Napoleon, Wenqing Yin, Nagla Elzinad, John Le, Mengwei Zhang, Xiaosheng Yang, Austin Morrissey, Murad Elsadawi, Qing Zhao, Scott E. Schaus, Ulla Hansen, Vipul C. Chitalia
Summary: This study reveals the Wnt inhibitory and CRC growth-suppressive effects of LSF inhibitors in CRC cells, providing a novel target in CRC therapeutics.
AMERICAN JOURNAL OF PATHOLOGY
(2022)