Frontiers in Plant Science (Dec 2020)
Single-Cell RNA Sequencing Efficiently Predicts Transcription Factor Targets in Plants
- Yunjie Xie,
- Yunjie Xie,
- Yunjie Xie,
- Yunjie Xie,
- Yunjie Xie,
- Yunjie Xie,
- Yunjie Xie,
- Yunjie Xie,
- Shenfei Jiang,
- Shenfei Jiang,
- Shenfei Jiang,
- Shenfei Jiang,
- Shenfei Jiang,
- Shenfei Jiang,
- Shenfei Jiang,
- Shenfei Jiang,
- Lele Li,
- Lele Li,
- Lele Li,
- Lele Li,
- Lele Li,
- Lele Li,
- Lele Li,
- Lele Li,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Xiangzhen Yu,
- Yupeng Wang,
- Yupeng Wang,
- Yupeng Wang,
- Yupeng Wang,
- Yupeng Wang,
- Yupeng Wang,
- Yupeng Wang,
- Yupeng Wang,
- Cuiqin Luo,
- Cuiqin Luo,
- Cuiqin Luo,
- Cuiqin Luo,
- Cuiqin Luo,
- Cuiqin Luo,
- Cuiqin Luo,
- Cuiqin Luo,
- Qiuhua Cai,
- Qiuhua Cai,
- Qiuhua Cai,
- Qiuhua Cai,
- Qiuhua Cai,
- Qiuhua Cai,
- Qiuhua Cai,
- Wei He,
- Wei He,
- Wei He,
- Wei He,
- Wei He,
- Wei He,
- Wei He,
- Hongguang Xie,
- Hongguang Xie,
- Hongguang Xie,
- Hongguang Xie,
- Hongguang Xie,
- Hongguang Xie,
- Hongguang Xie,
- Yanmei Zheng,
- Yanmei Zheng,
- Yanmei Zheng,
- Yanmei Zheng,
- Yanmei Zheng,
- Yanmei Zheng,
- Yanmei Zheng,
- Yanmei Zheng,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Huaan Xie,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang,
- Jianfu Zhang
Affiliations
- Yunjie Xie
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Yunjie Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Yunjie Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Yunjie Xie
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Yunjie Xie
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Yunjie Xie
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Yunjie Xie
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Yunjie Xie
- 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
- Shenfei Jiang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Shenfei Jiang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Shenfei Jiang
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Shenfei Jiang
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Shenfei Jiang
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Shenfei Jiang
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Shenfei Jiang
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Lele Li
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Lele Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Lele Li
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Lele Li
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Lele Li
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Lele Li
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Lele Li
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Lele Li
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, China
- Xiangzhen Yu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Xiangzhen Yu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Xiangzhen Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Xiangzhen Yu
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Xiangzhen Yu
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Xiangzhen Yu
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Xiangzhen Yu
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Xiangzhen Yu
- 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
- Yupeng Wang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Yupeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Yupeng Wang
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Yupeng Wang
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Yupeng Wang
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Yupeng Wang
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Yupeng Wang
- 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
- Cuiqin Luo
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Cuiqin Luo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Cuiqin Luo
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Cuiqin Luo
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Cuiqin Luo
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Cuiqin Luo
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Cuiqin Luo
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Qiuhua Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Qiuhua Cai
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Qiuhua Cai
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Qiuhua Cai
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Qiuhua Cai
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Qiuhua Cai
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Wei He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Wei He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Wei He
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Wei He
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Wei He
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Wei He
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Wei He
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Hongguang Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Hongguang Xie
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Hongguang Xie
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Hongguang Xie
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Hongguang Xie
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Hongguang Xie
- 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
- Yanmei Zheng
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Yanmei Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Yanmei Zheng
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Yanmei Zheng
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Yanmei Zheng
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Yanmei Zheng
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Yanmei Zheng
- 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
- Huaan Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Huaan Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Huaan Xie
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Huaan Xie
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Huaan Xie
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Huaan Xie
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Huaan Xie
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Huaan Xie
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, China
- Jianfu Zhang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Jianfu Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Jianfu Zhang
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Jianfu Zhang
- Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences and Technology, Fuzhou, China
- Jianfu Zhang
- Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China
- Jianfu Zhang
- Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Jianfu Zhang
- Base of South China, State Key Laboratory of Hybrid Rice, Fuzhou, China
- Jianfu Zhang
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, China
- DOI
- https://doi.org/10.3389/fpls.2020.603302
- Journal volume & issue
-
Vol. 11
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.
Keywords
