title: Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation.
abstract: Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution.
authors.affiliation: CAS Key Laboratory of Computational Biology and State Key Laboratory for Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Xu
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, 40225 Düsseldorf, Germany Network Analysis and Modeling, IPK Gatersleben, Correnstrasse 3, D-06466 Stadt Seeland, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Bräutigam
authors.affiliation: Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Andreas P M
authors.initials: AP
authors.lastname: Weber
authors.affiliation: CAS Key Laboratory of Computational Biology and State Key Laboratory for Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China zhuxinguang@picb.ac.cn.
authors.forename: Xin-Guang
authors.identifier: 0000-0002-4435-130X
authors.initials: XG
authors.lastname: Zhu
mesh_terms: D064527:Etiolation / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D017343:Genes, Plant / Q000235:genetics* / Q000502:physiology; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010788:Photosynthesis / Q000235:genetics* / Q000502:physiology; D018515:Plant Leaves / Q000502:physiology*; D003313:Zea mays / Q000235:genetics* / Q000502:physiology
keywords: C4 photosynthesis; cell specificity; cis element; etiolation; evolution; systems biology.