Jia‐Wei Wang

Chinese Academy of Sciences

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Guan-Dong Shang

Center for Excellence in Molecular Plant Sciences

Zhou-Geng Xu

Center for Excellence in Molecular Plant Sciences

Tian‐Qi Zhang

Center for Excellence in Molecular Plant Sciences

Fuxiang Wang

Center for Excellence in Molecular Plant Sciences

Jian Gao

Chinese Academy of Sciences

Sha Yu

Center for Excellence in Molecular Plant Sciences

Chuan‐Miao Zhou

Center for Excellence in Molecular Plant Sciences

Heng Lian

Center for Excellence in Molecular Plant Sciences

Xiao‐Ya Chen

Center for Excellence in Molecular Plant Sciences

Lian‐Yu Wu

Center for Excellence in Molecular Plant Sciences

Cooperative Institutions

Chinese Academy of Sciences

327

University of Chinese Academy of Sciences

183

Center for Excellence in Molecular Plant Sciences

128

Peking University

Zhejiang University

Nanjing Agricultural University

Shanghai Jiao Tong University

Sun Yat-sen University

Shanghai Institutes for Biological Sciences

Wuhan University

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Cell Quiescence Is the Fountain of Youth in Plants

SSRN Electronic Journal (2021)

Ying-Juan Cheng Guan-Dong Shang Geng-Zhou Xu Sha Yu Lian‐Yu Wu

What determines the rate at which a multicellular organism matures is a fundamental question in biology. In plants, the decline of miR156 with age serves as an intrinsic, evolutionarily conserved timer for the juvenile-to-adult phase transition. However, the way in which age regulates miR156 abundance is poorly understood. Here, we show that the rate of decline in miR156 is correlated with developmental age rather than chronological age. Mechanistically, we found that cell division in the apical meristem is a trigger for miR156 decline. The transcriptional activity of MIR156 genes is gradually attenuated by the deposition of the repressive histone mark H3K27me3 along with cell division. In perennial plants, the quiescent axillary shoot meristematic cells preserve their original epigenetic status at the MIR156 gene loci, thereby contributing to the formation of juvenile zones at the root crown. Our findings thus provide a plausible explanation of why the maturation program of a multicellular organism is unidirectional and irreversible, and uncover a molecular mechanism underlying the unique life-cycle strategy of long-lived perennial plants.

Fountain

10.2139/ssrn.3775177

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Root Genomics

CRC Press eBooks (2024)

Feng Zhou Heng Lian Jia‐Wei Wang

High-throughput single-cell RNA sequencing (scRNA-seq) enables the processing of thousands of cells in one experiment, thereby facilitating the characterization of cell heterogeneity in multicellular organisms with unprecedented detail. The application of scRNA-seq provides exciting opportunities to distinguish distinct cell populations with unique transcriptomic signatures and delineate continuous developmental trajectories. This chapter summarizes the recent research progress in building root cell atlas by single-cell transcriptome analyses in Arabidopsis. In combination with live imaging and reverse genetics, the resultant root cell atlas empowers us to delineate differentiation trajectories during root development, explore the cell-type specific response to environmental stimuli, understand shared and specific features of shoot and root apices at single-cell resolution, and probe conservation and divergence of the root cell types across the monocot-dicot divide. The implementation of single-cell epigenomics and spatial transcriptomics will uncover the regulatory basis underlying root development, physiology, and adaptation at unprecedented resolution. The generation of species-wide scRNA-seq datasets will further inform us of the evolutionary trajectories of the root in vascular plants. Moreover, the integration of scRNA-seq and genome-wide association studies will accelerate gene discovery for crop improvements in the future.

Root (linguistics)

10.1201/b23126-39

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Semi-rational design of an aromatic dioxygenase by substrate tunnel redirection

iScience (2024)

Jia‐Wei Wang Xingyu Ouyang Meng Sha Jiayi Li Liangxu Liu

Rational design

Dioxygenase

10.1016/j.isci.2024.111570

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Migration and Transformation of Nitrogen in Clay-Rich Soil Under Shallow Groundwater Depth: In Situ Experiment and Numerical Simulation

Water (2025)

Jinting Huang Q. Lv Zhan Yang Fang Pu Ge Song

Excessive use of nitrogen fertilizer in agricultural activities can easily induce nitrogen pollution in groundwater, which may deteriorate groundwater quality. Generally, nitrogen fertilizer passes through the unsaturated zone to groundwater. Therefore, it is of great significance to investigate the migration and transformation of nitrogen pollutants in unsaturated zones for the prevention and control of groundwater nitrogen pollution. Clay-rich soil is often considered a barrier layer to prevent pollutant leakage because of its lower relative permeability, while its prevention capacity is seldom reported under shallow groundwater table conditions. Motivated by this, an in situ experiment and numerical simulation were conducted to investigate the migration and transformation of nitrogen fertilizer in a clay-unsaturated zone with a shallow groundwater table. Systematic measurements and numerical simulation results revealed that nitrogen can pollute groundwater via the infiltration through clay-rich soil in the in situ experiment site. This finding clarified that the difference in hydraulic head under the shallow groundwater table, rather than soil permeability, is the dominant factor in controlling the downward migration of nitrogen pollutants in the clay-unsaturated zone. More importantly, the nitrogen migration is convection dominant during precipitation in this experiment, indicating nitrogen polluted groundwater much faster in humid climate areas. These findings suggest that nitrogen contaminates groundwater easily under shallow groundwater tables in humid climate areas, even with clay-rich soil texture.

Infiltration (HVAC)

10.3390/w17030427

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Additional file 1 of FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data

Figshare (2022)

Guan-Dong Shang Zhou-Geng Xu Mu-Chun Wan Fuxiang Wang Jia‐Wei Wang

Additional file 1. The number of related peaks for each gene.

Bioconductor

R package

Factor (programming language)

Omics

10.6084/m9.figshare.19555063

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Effects of magnetically treated Sedum alfredii seeds on the dissolved organic matter characteristics of Cd-contaminated soil during phytoextraction

Environmental Science and Pollution Research (2021)

Youjun Tang Shuaizhi Ji Dan Chen Jia‐Wei Wang Min Cao

10.1007/s11356-021-17312-w

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ISWI proteins participate in the genome‐wide nucleosome distribution in Arabidopsis

The Plant Journal (2014)

Guang Li Shujing Liu Jia‐Wei Wang Jianfeng He Hai Huang

Chromatin is a highly organized structure with repetitive nucleosome subunits. Nucleosome distribution patterns, which contain information on epigenetic controls, are dynamically affected by ATP-dependent chromatin remodeling factors (remodelers). However, whether plants have specific nucleosome distribution patterns and how plant remodelers contribute to the pattern formation are not clear. In this study we used the micrococcal nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in Arabidopsis thaliana. We demonstrated that the nucleosome distribution patterns of Arabidopsis are associated with the gene expression level, and have several specific characteristics that are different from those of animals and yeast. In addition, we found that remodelers in the A. thaliana imitation switch (AtISWI) subfamily are important for the formation of the nucleosome distribution pattern. Double mutations in the AtISWI genes, CHROMATIN REMODELING 11 (CHR11) and CHR17, resulted in the loss of the evenly spaced nucleosome pattern in gene bodies, but did not affect nucleosome density, supporting a previous idea that the primary role of ISWI is to slide nucleosomes in gene bodies for pattern formation.

Micrococcal nuclease

SWI/SNF

Subfamily

10.1111/tpj.12499

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Citations (95)

CCDC 1893722: Experimental Crystal Structure Determination

The Cambridge Structural Database (2019)

Jia‐Wei Wang Kosei Yamauchi Haihua Huang Jia‐Kai Sun Zhi‐Mei Luo

10.5517/ccdc.csd.cc21kkt0

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Association of Fruit and Seed Traits of Sapindus mukorossi Germplasm with Environmental Factors in Southern China

Forests (2017)

Caowen Sun Jia‐Wei Wang Jie Duan Guochun Zhao Xuehuang Weng

Sapindus mukorossi is widely distributed in tropical and subtropical areas of southern China; the seed kernel oil is potential biodiesel material, and the saponins extracted from fruit pericarp are very valuable efficient natural surfactants. Therefore, S. mukorossi is an ideal tree species for developing forestry bioenergy and multiple other products. In this study, 42 S. mukorossi fruits from mother trees were collected from 39 distinct locations in 12 Chinese provinces to infer fruit and seed trait responses to environmental factors. Canonical correspondence analysis (CCA) was conducted using 21 horticultural fruit traits and 10 environmental factors that represented different climatic and geographic conditions throughout southern China. CCA revealed well-developed patterns of natural phenotypic variation, and insight into the ecological factors that are potentially important in shaping this variation. The results presented here further elucidate the natural distribution and ecological adaptations of wild S. mukorossi resources, which will be valuable for S. mukorossi cultivation by helping identify ideal planting areas. The germplasm resources with extensive morphological variation can also contribute to S. mukorossi breeding in the future by helping develop new cultivars with high saponin yield.

Germ plasm

10.3390/f8120491

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CRY2 interacts with CIS1 to regulate thermosensory flowering via FLM alternative splicing

Nature Communications (2022)

Zhi-Wei Zhao Craig Dent Huafeng Liang Junqing Lv Guan-Dong Shang

Abstract Cryptochromes (CRYs) are evolutionarily conserved photolyase-like photoreceptors found in almost all species, including mammals. CRYs regulate transcription by modulating the activity of several transcription factors, but whether and how they affect pre-mRNA processing are unknown. Photoperiod and temperature are closely associated seasonal cues that influence reproductive timing in plants. CRYs mediate photoperiod-responsive floral initiation, but it is largely unknown whether and how they are also involved in thermosensory flowering. We establish here that blue light and CRY2 play critical roles in thermosensory flowering in Arabidopsis thaliana by regulating RNA alternative splicing (AS) to affect protein expression and development. CRY2 INTERACTING SPLICING FACTOR 1 (CIS1) interacts with CRY2 in a blue light–dependent manner and promotes CRY2–mediated thermosensory flowering. Blue light, CRYs, and CISs affect transcriptome-wide AS profiles, including those of FLOWERING LOCUS M ( FLM ), which is critical for temperature modulation of flowering. Moreover, CIS1 binds to the FLM pre-mRNA to regulate its AS, while CRY2 regulates the RNA-binding activity of CIS1. Thus, blue light regulates thermosensory flowering via a CRY2–CIS1–FLM signaling pathway that links flowering responses to both light and ambient temperature.

10.1038/s41467-022-34886-2

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Citations (30)