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Xie Y, Jiang S, Li L, Yu X, Wang Y, Luo C, Cai Q, He W, Xie H, Zheng Y, Xie H, Zhang J. Single-Cell RNA Sequencing Efficiently Predicts Transcription Factor Targets in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:603302. [PMID: 33424903 PMCID: PMC7793804 DOI: 10.3389/fpls.2020.603302] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/16/2020] [Indexed: 05/31/2023]
Abstract
Discovering transcription factor (TF) targets is necessary for the study of regulatory pathways, but it is hampered in plants by the lack of highly efficient predictive technology. This study is the first to establish a simple system for predicting TF targets in rice (Oryza sativa) leaf cells based on 10 × Genomics' single-cell RNA sequencing method. We effectively utilized the transient expression system to create the differential expression of a TF (OsNAC78) in each cell and sequenced all single cell transcriptomes. In total, 35 candidate targets having strong correlations with OsNAC78 expression were captured using expression profiles. Likewise, 78 potential differentially expressed genes were identified between clusters having the lowest and highest expression levels of OsNAC78. A gene overlapping analysis identified 19 genes as final candidate targets, and various assays indicated that Os01g0934800 and Os01g0949900 were OsNAC78 targets. Additionally, the cell profiles showed extremely similar expression trajectories between OsNAC78 and the two targets. The data presented here provide a high-resolution insight into predicting TF targets and offer a new application for single-cell RNA sequencing in plants.
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Affiliation(s)
- Yunjie Xie
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Shenfei Jiang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Lele Li
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiangzhen Yu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Yupeng Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Cuiqin Luo
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Wei He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Yanmei Zheng
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
| | - Huaan Xie
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianfu Zhang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, China
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