Article
Biochemistry & Molecular Biology
Xiaolin Zeng, Xinchen Lv, Rui Liu, Hang He, Shiqi Liang, Lixian Chen, Fan Zhang, Liu Chen, Yuehui He, Jiamu Du
Summary: The transcription factor CONSTANS (CO) forms a head-to-tail oligomeric configuration via its B-boxes to mediate the activation of florigen FLOWERING LOCUS T (FT) in long days. The multimerization of CO is crucial for its functionality.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Plant Sciences
Hongmiao Hu, Jiamu Du
Summary: This review focuses on the central role of histone methylation in regulating chromatin state and gene expression in Arabidopsis. It summarizes the current understanding of the dynamic regulation of histone methylation, with a particular emphasis on the histone methyltransferases and demethylases involved.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
News Item
Biochemistry & Molecular Biology
Sisi Li, Jiamu Du
Summary: A fungal TET dioxygenase homolog, CcTet, was found to have demethylase activity for both 5-methylcytosine (5mC) and N-6-methyladenine (6mA). Structure-based engineering of CcTet resulted in a 6mA-specific demethylase, which provides a useful tool for manipulating and studying 6mA.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xuan Du, Zhenlin Yang, Alfredo Jose Florez Ariza, Qian Wang, Guohui Xie, Sisi Li, Jiamu Du
Summary: This study determined the structure of maize RNA-DEPENDENT RNA POLYMERASE 2 (ZmRDR2) and found both active and inactive conformations, providing insights into the molecular mechanism of dsRNA synthesis during plant siRNA production.
Article
Multidisciplinary Sciences
Christine E. Peters, Ursula Schulze-Gahmen, Manon Eckhardt, Gwendolyn M. Jang, Jiewei Xu, Ernst H. Pulido, Melanie Ott, Or Gozani, Kliment A. Verba, Ruth Huettenhain, Jan E. Carette, Nevan J. Krogan
Summary: This study reports the structure of the interaction between Actin histidine methyltransferase SETD3 and the enterovirus CV-B3 2A protease, revealing the importance of the SET domain for virus replication. Mutations in key residues of the SET domain result in reduced binding to 2A and complete protection against enteroviral infection.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Chen Chen, June Ho Shin, Zhuoqing Fang, Kevin Brennan, Nina B. Horowitz, Kathleen L. Pfaff, Emma L. Welsh, Scott J. Rodig, Olivier Gevaert, Or Gozani, Ravindra Uppaluri, John B. Sunwoo
Summary: In head and neck squamous cell carcinoma (HNSCC), inactivating mutations in the histone methyltransferase NSD1 disproportionately contribute to tumor development and immune exclusion. Understanding the NSD1-mediated mechanism and targeting the histone-modifying enzyme KDM2A could enhance T-cell infiltration and suppress tumor growth in HNSCC.
Article
Multidisciplinary Sciences
Guohui Xie, Xuan Du, Hongmiao Hu, Sisi Li, Xiaofeng Cao, Steven E. Jacobsen, Jiamu Du
Summary: In this study, the structures of plant-specific polymerases Pols IV and V, which produce noncoding RNA in the RNA-directed DNA methylation pathway, were reported. The interaction between a conserved tyrosine residue of NRPE2 and double-stranded DNA branch in the transcription bubble suggests potential transcription stalling and attenuation of elongation. NRPE2 captures the nontemplate DNA strand to enhance backtracking and 3'-5' cleavage, allowing Pol V to maintain high fidelity. Furthermore, the structures provide insights into the mechanism of transcription stalling and enhanced backtracking by Pol V, supporting its function in tethering downstream factors for RNA-directed DNA methylation on chromatin.
Article
Biochemistry & Molecular Biology
Ricardo Mack, Or Gozani
Summary: The use of CRISPR technology and a high-content functional genomics screening platform sheds light on chromatin regulation and reveals a potential strategy for treating an aggressive type of leukemia.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Xuan Du, Zhenlin Yang, Guohui Xie, Changshi Wang, Laixing Zhang, Kaige Yan, Maojun Yang, Sisi Li, Jian-Kang Zhu, Jiamu Du
Summary: The plant-specific ROS1/DME enzyme family can directly remove 5-methyl-cytosine, resulting in efficient DNA demethylation. The cryo-electron microscopy structures of the Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA, and reaction intermediate were determined. The substrate 5-methyl-cytosine is flipped-out from the DNA duplex and recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions. The protonation states of the bases determine the substrate preference for 5-methyl-cytosine over T:G mismatch. The study provides insights into the substrate specificity and reaction mechanism of the ROS1/DME family of plant-specific DNA demethylases.
Article
Biochemistry & Molecular Biology
Deyue Yang, Fengli Zhao, Danling Zhu, Xi Chen, Xiangxiong Kong, Yufeng Wu, Min Chen, Jiamu Du, Li-Jia Qu, Zhe Wu
Summary: The RNA-binding protein RZ-1 and the polycomb complex 2 (PRC2) work together to silence ABA biosynthesis genes and ensure seed germination.
Article
Biology
Qian Wang, Yan Xue, Laixing Zhang, Zhenhui Zhong, Suhua Feng, Changshi Wang, Lifan Xiao, Zhenlin Yang, C. Jake Harris, Zhe Wu, Jixian Zhai, Maojun Yang, Sisi Li, Steven E. Jacobsen, Jiamu Du
Summary: A protocol was developed to evaluate the in vitro dicing activity of DCL3 in Arabidopsis, involving cutting pre-siRNA into a siRNA duplex which can be visualized and quantified using label-free fluorescence SYBR Gold on urea PAGE. This cost-effective and hazard-free method has the potential to be adapted for other Dicers and small RNAs.
Correction
Biochemistry & Molecular Biology
Daoheng Hu, Yiming Yu, Chun Wang, Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong, Lei Gong, Kejian Wang, Jixian Zhai
