Article
Plant Sciences
Zuntao Xu, Enze Li, Gan Xue, Cheng Zhang, Yachun Yang, Yong Ding
Summary: This study reveals that OsHUB2 represses the function of OsTrx1 and H3K4me3 levels at Ehd1, and suggests that OsHUB2-mediated H2B ubiquitination plays critical roles together with H3K4me3 in rice heading date regulation.
Article
Biochemistry & Molecular Biology
Prajakta Tathe, K. V. S. Rammohan Chowdary, Krushna Chandra Murmu, Punit Prasad, Subbareddy Maddika
Summary: In this study, the researchers discovered that the tyrosine phosphatase SHP-1 can dephosphorylate histone H2B and plays a critical role in transcription. SHP-1 dephosphorylates H2B at tyrosine 121, promoting H2B ubiquitination and maintaining basal autophagic flux. This study reveals the importance of SHP-1-regulated modification of H2B in eukaryotic transcription.
Article
Cell Biology
Liying Wang, Zhiliang Xu, Libin Wang, Chao Liu, Huafang Wei, Ruidan Zhang, Yinghong Chen, Lina Wang, Wenwen Liu, Sai Xiao, Wei Li, Wei Li
Summary: The study reveals that RNF20 is crucial for early stage somatic cell reprogramming, with Rnf20 knockout leading to failure in reprogramming at the initial stage. The absence of RNF20 affects the transcription of MET-related genes and early pluripotency genes, ultimately hindering the establishment of a pluripotent gene network.
CELL PROLIFERATION
(2021)
Article
Biochemistry & Molecular Biology
Fengling Lai, Yibin Cheng, Juan Zou, Haoyu Wang, Wang Zhu, Xin Wang, Hanhua Cheng, Rongjia Zhou
Summary: This study examined histone modifications in gonadal differentiation, identifying new modification sites and their relationship with different types of gonadal differentiation. The research also discovered a testis-enriched histone modification site associated with spermatogenesis, emphasizing the importance of histone modifications in the transcriptional regulation of sex-determining genes during gonadal development.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Cell Biology
Shinya Takahata, Saori Chida, Aoi Ohnuma, Motoyoshi Ando, Takahiro Asanuma, Yota Murakami
Summary: In heterochromatin, Spt16 recruitment is mediated by Pob3 and HP1/Swi6. Pob3 recruits Spt16 through its Spt16 dimerization and PH domains, while HP1/Swi6 recruits Spt16 through physical interaction of the Swi6 CSD and Spt16 peptidase-like domains.
Article
Biochemistry & Molecular Biology
Zhiheng Deng, Huasong Ai, Maoshen Sun, Zebin Tong, Yunxiang Du, Qian Qu, Liying Zhang, Ziyu Xu, Shixian Tao, Qiang Shi, Jia-Bin Li, Man Pan, Lei Liu
Summary: This study elucidates the mechanism of H2B monoubiquitylation and highlights the critical role of nucleosomal DNA in mediating E3 ligase recognition.
Article
Biochemistry & Molecular Biology
Zhiwen Zhu, Dongdong Li, Zeran Jia, Wenhao Zhang, Yuling Chen, Ruixue Zhao, Yan-Ping Zhang, Wen-Hong Zhang, Haiteng Deng, Yinqing Li, Wei Li, Shouhong Guang, Guangshuo Ou
Summary: Eukaryotic organisms adapt to environmental fluctuations by altering their epigenomic landscapes and transcriptional programs. Histone H2Bs are globally degraded in Caenorhabditis elegans during starvation, and the mechanisms underlying this degradation involve ubiquitin and ubiquitin-related enzymes. The retention of aberrant nucleosomal H2Bs leads to abnormal gene expression and impacts animal viability. Furthermore, the ubiquitin-proteasome system regulates chromosomal histone turnover in human cells.
Article
Biology
Ruben Rosas, Rhiannon R. Aguilar, Nina Arslanovic, Anna Seck, Duncan J. Smith, Jessica K. Tyler, Mair E. A. Churchill
Summary: The histone chaperone CAF-1 deposits histone H3/H4 dimers onto newly replicated DNA to form the central core of the nucleosome tetrasome. The KER SAH region of CAF-1 plays a crucial role in ensuring the assembly of tetrasomes by linking functional domains within CAF-1 with structural precision.
Article
Microbiology
Ruoyan Liu, Xiaoyu Chen, Fujie Zhao, Yixuan Jiang, Zhenguo Lu, Huining Ji, Yuanyuan Feng, Junqiang Li, Heng Zhang, Jianting Zheng, Jing Zhang, Youbao Zhao
Summary: The COMPASS protein complex plays a crucial role in regulating gene expression and virulence in Cryptococcus neoformans. The core subunits Set1, Bre2, Swd1, and Swd3 act as a catalytic core and control the development and virulence of the fungus.
Article
Multidisciplinary Sciences
Nathan J. VanDusen, Julianna Y. Lee, Weiliang Gu, Catalina E. Butler, Isha Sethi, Yanjiang Zheng, Justin S. King, Pingzhu Zhou, Shengbao Suo, Yuxuan Guo, Qing Ma, Guo-Cheng Yuan, William William Pu
Summary: The study utilized in vivo somatic Cas9 mutagenesis in mice to conduct a forward genetic screen for regulators of cardiomyocyte maturation, identifying transcriptional regulators such as RNF20 and RNF40. Mechanistic studies showed that these regulators control dynamic gene expression changes essential for cardiomyocyte maturation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Robyn Laura Kosinsky, Maria Zerche, Ana Patricia Kutschat, Asha Nair, Zhenqing Ye, Dominik Saul, Maximilian von Heesen, Jessica J. Friton, Ana Carolina Schwarzer, Nadia Paglilla, Shehzad Z. Sheikh, Florian Wegwitz, Zhifu Sun, Michael Ghadimi, Rodney D. Newberry, R. Balfour Sartor, William A. Faubion, Steven A. Johnsen
Summary: Despite the identification of genetic factors linked to IBD susceptibility, the mechanisms behind it are still unclear. The RNF20/RNF40/H2Bub1 axis plays a critical role in promoting intestinal inflammation in IBD patients and mouse models, revealing their importance as regulators of IBD.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Oncology
Lucile M. Jeusset, Kirk J. McManus
Summary: Monoubiquitination of histone H2B on lysine 120 plays a crucial role in various biological processes. Aberrant regulation of H2Bub1 can lead to transcriptional reprogramming and genome instability, thereby promoting oncogenesis. Understanding the misregulation of H2Bub1 may reveal novel drug targets and therapeutic strategies for cancer treatment.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Genetics & Heredity
Hadar Tzemach Korenfeld, Adi Avram-Shperling, Yifat Zukerman, Anais Iluz, Hanna Boocholez, Lilach Ben-Shimon, Shay Ben-Aroya
Summary: Mono-ubiquitination of histone H2B (H2B-Ub1) plays a central role in regulating biological processes such as the DNA damage response, gene transcription, and DNA replication. This study demonstrates that deubiquitination of H2B-Ub1 is essential for recovery from replication stress.
Article
Multidisciplinary Sciences
Jimin Li, Jingyu Zhao, Xiaoli Gan, Yanyan Wang, Donghao Jiang, Liang Chen, Fangwei Wang, Jingyan Xu, Huadong Pei, Jun Huang, Xuefeng Chen
Summary: The interaction between the single-strand DNA-binding factor Replication protein A (RPA) and Ring finger protein 20 (RNF20) is important for chromosome segregation and DNA repair. RPA recruits RNF20 to mitotic centromeres and chromosomal breaks, leading to proper loading of repair proteins and maintenance of genome stability. The RPA-RNF20-SNF2H cascade plays a crucial role in preserving genome stability by coupling histone modification to chromosome segregation and DNA repair.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Guangxue Liu, Jiaqi Yan, Xuejie Wang, Junliang Chen, Xin Wang, Yang Dong, Simin Zhang, Xiaoli Gan, Jun Huang, Xuefeng Chen
Summary: The study reveals that the ssDNA binding factor RPA mediates the coupling of Bre1-mediated H2Bub with DNA replication and repair processes, ensuring the proper functioning of H2Bub in these contexts. Disruption of the interaction between RPA and Bre1 leads to instability of H2Bub, affecting DNA replication, repair, and genome stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Kun-Hsing Yu, Tsung-Lu Michael Lee, Chi-Shiang Wan, Yu-Ju Chen, Christopher Re, Samuel C. Kou, Jung-Hsien Chiang, Isaac S. Kohane, Michael Snyder
JOURNAL OF PROTEOME RESEARCH
(2018)
Article
Biochemical Research Methods
Kun-Hsing Yu, Tsung-Lu Michael Lee, Yu-Ju Chen, Christopher Re, Samuel C. Kou, Jung-Hsien Chiang, Michael Snyder, Isaac S. Kohane
JOURNAL OF PROTEOME RESEARCH
(2018)
Article
Health Care Sciences & Services
Chi-Shiang Wang, Pei-Ju Lin, Ching-Lan Cheng, Shu-Hua Tai, Yea-Huei Kao Yang, Jung-Hsien Chiang
JOURNAL OF MEDICAL INTERNET RESEARCH
(2019)
Article
Multidisciplinary Sciences
Robert Kueffner, Neta Zach, Maya Bronfeld, Raquel Norel, Nazem Atassi, Venkat Balagurusamy, Barbara Di Camillo, Adriano Chio, Merit Cudkowicz, Donna Dillenberger, Javier Garcia-Garcia, Orla Hardiman, Bruce Hoff, Joshua Knight, Melanie L. Leitner, Guang Li, Lara Mangravite, Thea Norman, Liuxia Wang, Rached Alkallas, Catalina Anghel, Jeanne Avril, Jaume Bacardit, Barbara Balser, John Balser, Yoav Bar-Sinai, Noa Ben-David, Eyal Ben-Zion, Robin Bliss, Jialu Cai, Anatoly Chernyshev, Jung-Hsien Chiang, Davide Chicco, Bhavna Ahuja Nicole Corriveau, Junqiang Dai, Yash Deshpande, Eve Desplats, Joseph S. Durgin, Shadrielle Melijah G. Espiritu, Fan Fan, Philippe Fevrier, Brooke L. Fridley, Adam Godzik, Agnieszka Golinska, Jonathan Gordon, Stefan Graw, Yuelong Guo, Tim Herpelinck, Julia Hopkins, Barbara Huang, Jeremy Jacobsen, Samad Jahandideh, Jouhyun Jeon, Wenkai Ji, Kenneth Jung, Alex Karanevich, Devin C. Koestler, Michael Kozak, Christoph Kurz, Christopher Lalansingh, Thomas Larrieu, Nicola Lazzarini, Boaz Lerner, Wojciech Lesinski, Xiaotao Liang, Xihui Lin, Jarrett Lowe, Lester Mackey, Richard Meier, Wenwen Min, Krzysztof Mnich, Violette Nahmias, Janelle Noel-MacDonnell, Adrienne O'Donnell, Susan Paadre, Ji Park, Aneta Polewko-Klim, Rama Raghavan, Witold Rudnicki, Ehsan Saghapour, Jean-Bernard Salomond, Kris Sankaran, Dorota Sendorek, Vatsal Sharan, Yu-Jia Shiah, Jean-Karl Sirois, Dinithi N. Sumanaweera, Joseph Usset, Yeeleng S. Vang, Celine Vens, Dave Wadden, David Wang, Wing Chung Wong, Xiaohui Xie, Zhiqing Xu, Hsih-Te Yang, Xiang Yu, Haichen Zhang, Li Zhang, Shihua Zhang, Shanfeng Zhu, Jinfeng Xiao, Wen-Chieh Fang, Jian Peng, Chen Yang, Huan-Jui Chang, Gustavo Stolovitzky
SCIENTIFIC REPORTS
(2019)
Article
Computer Science, Artificial Intelligence
Pei-Yi Hao, Weng-Hang Cheang, Jung-Hsien Chiang
Article
Health Care Sciences & Services
Kun-Hsing Yu, Tsung-Lu Michael Lee, Ming-Hsuan Yen, S. C. Kou, Bruce Rosen, Jung-Hsien Chiang, Isaac S. Kohane
JOURNAL OF MEDICAL INTERNET RESEARCH
(2020)
Article
Cardiac & Cardiovascular Systems
Mu-Shiang Huang, Chi-Shiang Wang, Jung-Hsien Chiang, Ping-Yen Liu, Wei-Chuan Tsai
Article
Health Care Sciences & Services
Ping-Yen Liu, Yi-Shan Tsai, Po-Lin Chen, Huey-Pin Tsai, Ling-Wei Hsu, Chi-Shiang Wang, Nan-Yao Lee, Mu-Shiang Huang, Yun-Chiao Wu, Wen-Chien Ko, Yi-Ching Yang, Jung-Hsien Chiang, Meng-Ru Shen
JOURNAL OF MEDICAL INTERNET RESEARCH
(2020)
Article
Computer Science, Artificial Intelligence
Chi-Shiang Wang, Bo-Syun Chen, Jung-Hsien Chiang
Summary: The study focuses on capturing user preferences through a topic diversity discovering model and integrating it with a Bayesian personalized ranking model to create a novel recommender system. Experimental results show that the system achieved high Hit Ratio@10 on three different datasets, confirming that the TDD-BPR recommender system can better understand user preferences and provide better recommendations.
Article
Computer Science, Artificial Intelligence
Jung-Hsien Chiang, Chung-Yao Ma, Chi-Shiang Wang, Pei-Yi Hao
Summary: Recommendation systems have become more important due to the abundance of information on the internet. This study proposes a novel recommendation system that adapts to users' changing preferences by using context factors and attention mechanisms. Experimental results show that this context-aware recommendation model outperforms traditional methods.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Computer Science, Artificial Intelligence
Pei-Yi Hao, Jung-Hsien Chiang, Yu-De Chen
Summary: This paper proposes a novel possibilistic classification algorithm using support vector machines (SVMs) to effectively handle uncertain information and improve classification performance. The algorithm aims at finding a maximal-margin fuzzy hyperplane based on possibility theory and solves a fuzzy mathematical optimization problem. The proposed algorithm retains the advantages of fuzzy set theory and SVM theory, and it is more robust for handling outliers. Experimental results demonstrate the satisfactory generalization accuracy and ability to describe inherent vagueness in the given dataset.
Article
Biochemical Research Methods
Sina Abdollahi, Peng-Chan Lin, Jung-Hsien Chiang
Summary: Mutational signatures help identify cancer-associated genes and guide precision medicine. The pattern of mutations varies in different cancer types and can be used to differentiate cancer types. In this study, trinucleotide mutational patterns and gene mutational signatures are used to identify cancer-associated genes, which are evaluated using survival and gene expression analysis. The proposed DiaDeL model, a deep learning-based binary classifier, outperforms other methods in accuracy and AUC.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Peng-Chan Lin, Hui-O Chen, Chih-Jung Lee, Yu-Min Yeh, Meng-Ru Shen, Jung-Hsien Chiang
Summary: The study utilized germline DSVs and DSV immune-related association tumor microenvironment (TME) to predict cancer risk and prognosis, identifying 671 DSVs that could predict cancer risk and determining some DSVs relevant to colorectal cancer.
Proceedings Paper
Computer Science, Artificial Intelligence
Chi-Shiang Wang, Hung-Chun Chen, Jung-Hsien Chiang
2019 INTERNATIONAL CONFERENCE ON TECHNOLOGIES AND APPLICATIONS OF ARTIFICIAL INTELLIGENCE (TAAI)
(2019)
Article
Mathematical & Computational Biology
Chia-Jung Yang, Jung-Hsien Chiang
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2018)