Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

Chun-Ping Yu, Chun-Chang Chen, Yao-Ming Chang, Wen-Yu Liu, Hsin-Hung Lin, Jinn-Jy Lin, Hsiang-June Chen, Yu-Ju Lu, Yi-Hsuan Wu, Mei-Yeh-Jade Lu, Chen-Hua Lu, Arthur-Chun-Chieh Shih, Maurice-Sun-Ben Ku, Shin-Han Shiu, Shu-Hsing Wu, Wen-Hsiung Li

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)E2477-E2486
JournalProceedings of the National Academy of Sciences of the United States of America
Volume112
Issue number19
DOIs
Publication statusPublished - 2015
Externally publishedYes

Keywords

  • Cis binding site
  • Coexpressed genes
  • Maize transcriptomes
  • transcription factor
  • transcriptome
  • Arabidopsis
  • Article
  • binding site
  • controlled study
  • down regulation
  • gene expression
  • gene ontology
  • gene sequence
  • genetic conservation
  • genetic transcription
  • germination
  • in vitro study
  • leaf development
  • maize
  • molecular dynamics
  • multigene family
  • nonhuman
  • plant gene
  • plant leaf
  • plant seed
  • prediction
  • priority journal
  • rice
  • upregulation
  • Zea mays

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  • Cite this

    Yu, C-P., Chen, C-C., Chang, Y-M., Liu, W-Y., Lin, H-H., Lin, J-J., Chen, H-J., Lu, Y-J., Wu, Y-H., Lu, M-Y-J., Lu, C-H., Shih, A-C-C., Ku, M-S-B., Shiu, S-H., Wu, S-H., & Li, W-H. (2015). Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 112(19), E2477-E2486. https://doi.org/10.1073/pnas.1500605112