Article
Plant Sciences
Guanqun Wang, Xiaozheng Li, Wei Shen, Man-Wah Li, Mingkun Huang, Jianhua Zhang, Haoxuan Li
Summary: This study characterized the open chromatin regions (OCRs) in rice pistils and anthers using transposase-accessible chromatin sequencing. The results showed that there were more OCRs in pistils than in anthers, and these OCRs were enriched in gene transcription start sites and tightly associated with gene expression. Transcription factor binding motifs were also found to be enriched at these OCRs, validating their role in gene regulation. Additionally, the study found that the open chromatin of pistils and anthers responded differently to low temperature.
Article
Biochemical Research Methods
Zongbao Sun, Jiahao Qi, Ye Shen, Ning Yang, Shuhua Liu, Aiying Wang, Cilin Wang, Jian Tang
Summary: We have successfully developed a simple, portable microfluidic test platform for rapid detection of rice false smut (RFS). The platform integrates spore purification, nucleic acid release, and amplification into one chip. We achieved spore collection efficiency of approximately 78% and 100% specificity with a detection limit of 100 copies/reaction. The proposed microfluidic chip offers a faster and easier alternative to traditional PCR methods for field detection of RFS.
Article
Plant Sciences
Mohammad Reza Atighi, Bruno Verstraeten, Tim De Meyer, Tina Kyndt
Summary: Epigenetic processes, particularly histone modifications, play a crucial role in plant-nematode interactions, with a specific focus on H3K9 targeting plant defence-related genes.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Multidisciplinary Sciences
Longfei Wang, Shuai Cao, Peitong Wang, Kening Lu, Qingxin Song, Fang-Jie Zhao, Z. Jeffrey Chen
Summary: Polyploidy enhances salt tolerance in tetraploid rice by reducing sodium uptake and epigenetic regulation of JA-related genes. This leads to increased expression of stress-responsive genes in the JA pathway, higher levels of JA signaling, and feedback regulation between hypomethylation and hypermethylation to promote stress adaptation in polyploid plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael Love, Mikhail G. Dozmorov
Summary: Exclusion regions are abnormal sections of reference genomes where short sequencing reads pile up. Removing reads overlapping these regions improves biological signal, particularly in differential analysis. Multiple exclusion region sets have been created by labs, primarily available through ENCODE and Github, causing uncertainty in which sets to use. Additionally, gap regions like centromeres, telomeres, and short arms pose further considerations when generating exclusion sets.
Article
Environmental Sciences
Jinyao Yan, Tao Ren, Kunkun Wang, Tinghong Ye, Yi Song, Rihuan Cong, Xiaokun Li, Zhifeng Lu, Jianwei Lu
Summary: Identifying major sources and critical periods of P loss is important for reducing P loss in agricultural fields. A study found that applying P fertilizer increased P concentration in the water of a rice-oilseed rape rotation, and the initial 10 days after fertilization in the rice season were critical for reducing P runoff loss.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R. Zhang
Summary: The epigenetic control of gene expression is highly cell-type and context specific, and can be broken down into modular components by a transcription factor activating or repressing the target gene expression. A new nonparametric approach, TRIPOD, is proposed to detect and characterize the relationships between TF, target gene, and TF binding site accessibility using single-cell RNA and ATAC multiomic data.
Article
Plant Sciences
Jo-Wei Allison Hsieh, Pearl Chang, Lin-Yun Kuang, Yue-Ie C. Hsing, Pao-Yang Chen
Summary: During transgenic plant production, tissue culture often leads to unpredictable phenotypes due to epigenetic and genetic changes. Specific treatments during rice transformation processes have unknown impacts on DNA methylation and transcriptional variations. This study reveals that individual transformation treatments affect genome-wide DNA methylation and gene expression, independent of tissue culture. The findings highlight the specificity of these treatment impacts and their potential association with somaclonal variations.
Article
Plant Sciences
Patrick E. Hayes, Getnet D. Adem, Juan Pariasca-Tanaka, Matthias Wissuwa
Summary: The study highlights the importance of reducing lipid-P investment in improving PUE in rice, without compromising photosynthesis. Low-P plants showed reduced investment in inorganic-P and lipid-P, while whole-plant PUE was associated with preferential allocation of resources to the youngest mature leaves.
Article
Multidisciplinary Sciences
M. Asaduzzaman Prodhan, Juan Pariasca-Tanaka, Yoshiaki Ueda, Patrick E. Hayes, Matthias Wissuwa
Summary: Phosphorus (P) is essential for plants, but most rice growing lands lack adequate P, leading to the need for multiple P fertiliser applications. Developing P-efficient rice varieties that require less P is important, and research on genetic factors underlying P-use efficiency (PUE) in rice is ongoing. Comparative transcriptome analysis between a P-efficient landrace DJ123 and a P-inefficient modern cultivar IR64 revealed that DJ123 rapidly responds to low P conditions by inducing specific genes, potentially contributing to its high PUE. These findings provide a valuable foundation for elucidating PUE mechanisms in rice and could aid in the development of efficient modern rice varieties.
SCIENTIFIC REPORTS
(2022)
Editorial Material
Plant Sciences
Hilary Joan Rogers
Summary: The epigenetic reprogramming through genome-wide histone H3 acetylation (H3K9ac) plays an important role in rice leaf senescence.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Hong Qiu, Haobo Li, Ruiwen Fan, Yang Song, Xuan Pan, Chunhui Zhang, Jing Li
Summary: By analyzing the DNA methylation profile of the thymus in rhesus macaques, we found that DNA methylation plays an important role in the aging and functional changes of the thymus, especially in immunity and coagulation. The changes in methylation levels of certain genes in the thymus are closely associated with their expression levels and affect the thymus function, such as immune function and coagulation function. Moreover, the changes in methylation levels and gene expression levels of T cell development genes and thymogenic hormone genes are closely related to the decline in differentiation, activation, and maturation of T cells in adult thymuses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mengyao Wang, Jianbo Wang
Summary: The study suggests that the flag leaf heterosis of indica x japonica inter-subspecific hybrid rice is related to leaf area, gene expression pattern, and allele-specific expression, potentially influenced by DNA methylation differences. The genetic and epigenetic molecular mechanisms of heterosis in this hybrid rice remain not fully understood, but the analysis of gene expression and epigenetic regulation provides insights into potential mechanisms. Photosynthetic functions and DNA methylation were found to play crucial roles in regulating gene expression levels and influencing heterosis in the inter-subspecific hybrid rice.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Agronomy
Thanh Tung Nguyen, Yuka Sasaki, Mitsuhiko Katahira, Dhirendranath Singh
Summary: The study found that applying cow manure in phosphorus-rich soils can reduce the amount of phosphorus fertilizer needed, maintain soil phosphorus levels, and achieve similar rice growth and yield to that of phosphorus fertilizer.
Article
Multidisciplinary Sciences
Jia Zhou, Qinli Hu, Xinlong Xiao, Deqiang Yao, Shenghong Ge, Jin Ye, Haojie Li, Rujie Cai, Renyang Liu, Fangang Meng, Chao Wang, Jian-Kang Zhu, Mingguang Lei, Weiman Xing
Summary: SPX1 protein binds to InsP(6) to inhibit the activity of PHR2 by disrupting PHR2 dimers and forming a SPX1-PHR2 complex, thereby maintaining phosphate homeostasis. This dual mechanism attenuates dimerization and DNA binding activities of PHR2.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Quanxiu Wang, Weibo Xie, Hongkun Xing, Ju Yan, Xiangzhou Meng, Xinglei Li, Xiangkui Fu, Jiuyue Xu, Xingming Lian, Sibin Yu, Yongzhong Xing, Gongwei Wang
Article
Multidisciplinary Sciences
Weibo Xie, Gongwei Wang, Meng Yuan, Wen Yao, Kai Lyu, Hu Zhao, Meng Yang, Pingbo Li, Xing Zhang, Jing Yuan, Quanxiu Wang, Fang Liu, Huaxia Dong, Lejing Zhang, Xinglei Li, Xiangzhou Meng, Wan Zhang, Lizhong Xiong, Yuqing He, Shiping Wang, Sibin Yu, Caiguo Xu, Jie Luo, Xianghua Li, Jinghua Xiao, Xingming Lian, Qifa Zhang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Plant Sciences
Jiali Yan, Peitong Wang, Peng Wang, Meng Yang, Xingming Lian, Zhong Tang, Chao-Feng Huang, David E. Salt, Fang Jie Zhao
PLANT CELL AND ENVIRONMENT
(2016)
Article
Multidisciplinary Sciences
Xiaorong Fan, Zhong Tang, Yawen Tan, Yong Zhang, Bingbing Luo, Meng Yang, Xingming Lian, Qirong Shen, Anthony John Miller, Guohua Xu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biochemistry & Molecular Biology
Hao Zhou, Pingbo Li, Weibo Xie, Saddam Hussain, Yibo Li, Duo Xia, Hu Zhao, Shengyuan Sun, Junxiao Chen, Hong Ye, Jun Hou, Da Zhao, Guanjun Gao, Qinglu Zhang, Gongwei Wang, Xingming Lian, Jinghua Xiao, Sibin Yu, Xianghua Li, Yuqing He
Article
Plant Sciences
Ying Ye, Peng Li, Tangqian Xu, Liting Zeng, Deng Cheng, Meng Yang, Jie Luo, Xingming Lian
FRONTIERS IN PLANT SCIENCE
(2017)
Article
Plant Sciences
Yuanyuan Zhang, Kai Chen, Fang-Jie Zhao, Cuiju Sun, Cheng Jin, Yuheng Shi, Yangyang Sun, Yuan Li, Meng Yang, Xinyu Jing, Jie Luo, Xingming Lian
Article
Plant Sciences
Meng Yang, Yuanyuan Zhang, Lejing Zhang, Jintao Hu, Xing Zhang, Kai Lu, Huaxia Dong, Dujun Wang, Fang-Jie Zhao, Chao-Feng Huang, Xingming Lian
JOURNAL OF EXPERIMENTAL BOTANY
(2014)
Article
Genetics & Heredity
Wei Chen, Yanqiang Gao, Weibo Xie, Liang Gong, Kai Lu, Wensheng Wang, Yang Li, Xianqing Liu, Hongyan Zhang, Huaxia Dong, Wan Zhang, Lejing Zhang, Sibin Yu, Gongwei Wang, Xingming Lian, Jie Luo
Article
Biochemistry & Molecular Biology
Hu Zhao, Wen Yao, Yidan Ouyang, Wanneng Yang, Gongwei Wang, Xingming Lian, Yongzhong Xing, Lingling Chen, Weibo Xie
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biochemistry & Molecular Biology
Chunmei Zhu, Qiang Peng, Debao Fu, Dongxia Zhuang, Yiming Yu, Min Duan, Weibo Xie, Yaohui Cai, Yidang Ouyan, Xingming Lian, Changyin Wu
Article
Biochemical Research Methods
Hongmei Cai, Weibo Xie, Xingming Lian
PLANT MOLECULAR BIOLOGY REPORTER
(2013)
Article
Multidisciplinary Sciences
Ying Ye, Jing Yuan, Xiaojian Chang, Meng Yang, Lejing Zhang, Kai Lu, Xingming Lian
Article
Biochemistry & Molecular Biology
Meng Yang, Kai Lu, Fang-Jie Zhao, Weibo Xie, Priya Ramakrishna, Guangyuan Wang, Qingqing Du, Limin Liang, Cuiju Sun, Hu Zhao, Zhanyi Zhang, Zonghao Liu, Jingjing Tian, Xin-Yuan Huang, Wensheng Wang, Huaxia Dong, Jintao Hu, Luchang Ming, Yongzhong Xing, Gongwei Wang, Jinhua Xiao, David E. Salt, Xingming Lian
Article
Biotechnology & Applied Microbiology
Wen Yao, Guangwei Li, Hu Zhao, Gongwei Wang, Xingming Lian, Weibo Xie