Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize
Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. I...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/159827 |
| _version_ | 1855529787657814016 |
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| author | Luo, Bowen Zhang, Ziqi Li, Binyang Zhang, Haiying Ma, Junchi Li, Jing Han, Zheng Zhang, Chong Zhang, Shuhao Yu, Ting Zhang, Guidi Ma, Peng Lan, Yuzhou Zhang, Xiao Liu, Dan Wu, Ling Gao, Duojiang Gao, Shiqiang Su, Shunzong Zhang, Xuecai Gao, Shibin |
| author_browse | Gao, Duojiang Gao, Shibin Gao, Shiqiang Han, Zheng Lan, Yuzhou Li, Binyang Li, Jing Liu, Dan Luo, Bowen Ma, Junchi Ma, Peng Su, Shunzong Wu, Ling Yu, Ting Zhang, Chong Zhang, Guidi Zhang, Haiying Zhang, Shuhao Zhang, Xiao Zhang, Xuecai Zhang, Ziqi |
| author_facet | Luo, Bowen Zhang, Ziqi Li, Binyang Zhang, Haiying Ma, Junchi Li, Jing Han, Zheng Zhang, Chong Zhang, Shuhao Yu, Ting Zhang, Guidi Ma, Peng Lan, Yuzhou Zhang, Xiao Liu, Dan Wu, Ling Gao, Duojiang Gao, Shiqiang Su, Shunzong Zhang, Xuecai Gao, Shibin |
| author_sort | Luo, Bowen |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics. |
| format | Journal Article |
| id | CGSpace159827 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1598272025-10-26T12:53:00Z Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize Luo, Bowen Zhang, Ziqi Li, Binyang Zhang, Haiying Ma, Junchi Li, Jing Han, Zheng Zhang, Chong Zhang, Shuhao Yu, Ting Zhang, Guidi Ma, Peng Lan, Yuzhou Zhang, Xiao Liu, Dan Wu, Ling Gao, Duojiang Gao, Shiqiang Su, Shunzong Zhang, Xuecai Gao, Shibin phosphorus maize chromatin gene expression dna rna Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics. 2024-01 2024-11-15T14:54:41Z 2024-11-15T14:54:41Z Journal Article https://hdl.handle.net/10568/159827 en Limited Access Wiley Luo, B., Zhang, Z., Li, B., Zhang, H., Ma, J., Li, J., Han, Z., Zhang, C., Zhang, S., Yu, T., Zhang, G., Ma, P., Lan, Y., Zhang, X., Liu, D., Wu, L., Gao, D., Gao, S., Su, S., . . . Gao, S. (2023). Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize. The Plant Journal, 117(1), 33-52. https://doi.org/10.1111/tpj.16468 |
| spellingShingle | phosphorus maize chromatin gene expression dna rna Luo, Bowen Zhang, Ziqi Li, Binyang Zhang, Haiying Ma, Junchi Li, Jing Han, Zheng Zhang, Chong Zhang, Shuhao Yu, Ting Zhang, Guidi Ma, Peng Lan, Yuzhou Zhang, Xiao Liu, Dan Wu, Ling Gao, Duojiang Gao, Shiqiang Su, Shunzong Zhang, Xuecai Gao, Shibin Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize |
| title | Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize |
| title_full | Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize |
| title_fullStr | Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize |
| title_full_unstemmed | Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize |
| title_short | Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize |
| title_sort | chromatin remodeling analysis reveals the rddm pathway responds to low phosphorus stress in maize |
| topic | phosphorus maize chromatin gene expression dna rna |
| url | https://hdl.handle.net/10568/159827 |
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