Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors.
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development.
Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan 40227;
Chun-Ping
CP
Yu
Biodiversity Research Center.
Sean Chun-Chang
SC
Chen
Biodiversity Research Center.
Yao-Ming
YM
Chang
Biodiversity Research Center.
Wen-Yu
WY
Liu
Biodiversity Research Center.
Hsin-Hung
HH
Lin
Biodiversity Research Center, Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan 300;
Jinn-Jy
JJ
Lin
Biodiversity Research Center.
Hsiang June
HJ
Chen
Biodiversity Research Center.
Yu-Ju
YJ
Lu
Biodiversity Research Center.
Yi-Hsuan
YH
Wu
Biodiversity Research Center.
Mei-Yeh Jade
MY
Lu
Institute of Information Science, and.
Chen-Hua
CH
Lu
Institute of Information Science, and.
Arthur Chun-Chieh
AC
Shih
Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600; School of Biological Sciences, Washington State University, Pullman, WA 99164;
Maurice Sun-Ben
MS
Ku
Department of Plant Biology, Michigan State University, East Lansing, MI 48824; and shius@msu.edu shuwu@gate.sinica.edu.tw whli@uchicago.edu.
Shin-Han
SH
Shiu
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 115; shius@msu.edu shuwu@gate.sinica.edu.tw whli@uchicago.edu.
Shu-Hsing
SH
Wu
Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan 40227; Biodiversity Research Center, Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 shius@msu.edu shuwu@gate.sinica.edu.tw whli@uchicago.edu.
Wen-Hsiung
WH
Li
D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics; D001665:Binding Sites; D019295:Computational Biology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005810:Multigene Family; D012275:Oryza / Q000235:genetics; D010788:Photosynthesis; D018515:Plant Leaves / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics*
D014157:Transcription Factors
cis binding site; coexpressed genes; maize transcriptomes