Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

文化大學機構典藏 CCUR > 環境規劃暨生物資源學院 > 農學院 > 園藝暨生物技術學系 > 期刊論文 > Item 987654321/44650

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题名:	Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes
作者:	Chang, YM (Chang, Yao-Ming) Lin, HH (Lin, Hsin-Hung) Liu, WY (Liu, Wen-Yu) Yu, CP (Yu, Chun-Ping) Chen, HJ (Chen, Hsiang-June) Wartini, PP (Wartini, Putu Puja) Kao, YY (Kao, Yi-Ying) Wu, YH (Wu, Yeh-Hua) Lin, JJ (Lin, Jinn-Jy) Lu, MYJ (Lu, Mei-Yeh Jade) Tu, SL (Tu, Shih-Long) Wu, SH (Wu, Shu-Hsing) Shiu, SH (Shiu, Shin-Han) Ku, MSB (Ku, Maurice S. B.) Li, WH (Li, Wen-Hsiung)
贡献者:	園藝系
关键词:	SEED-GERMINATION REGULATORY DNA KRANZ ANATOMY C-4 DYNAMICS EXPRESSION LEAVES DIFFERENTIATION PHOTOSYNTHESIS MESOPHYLL
日期:	2019-02-19
上传时间:	2019-06-25 13:28:37 (UTC+8)
摘要:	Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light-dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C-4 plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C-4 enzyme genes and RUBISCO SMALL SUBUNIT2. Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C-4 photosynthesis.
關聯:	PNAS February 19, 2019 116 (8) 3091-3099
显示于类别:	[園藝暨生物技術學系] 期刊論文

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