The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network

Stuart Meier, Chris Gehring, Cameron Ross MacPherson, Mandeep Kaur, Monique Maqungo, Sheela Reuben, Samson Muyanga, Ming Der Shih, Fu Jin Wei, Samart Wanchana, Ramil Mauleon, Aleksandar Radovanovic, Richard Bruskiewich, Tsuyoshi Tanaka, Bijayalaxmi Mohanty, Takeshi Itoh, Rod Wing, Takashi Gojobori, Takuji Sasaki, Sanjay SwarupYue ie Hsing, Vladimir B. Bajic

Research output: Contribution to journalArticle

12 Scopus citations

Abstract

Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing genes that function coherently during specific cellular responses. To find the coexpressing genes we propose an ab initio method that identifies motif families in promoters of target gene groups, map these families to the promoters of all genes in the genome, and determine the best matches of each of the target group gene promoters with all other promoters. When the method was tested in rice starting from a group of co-expressing Late Embryogenesis Abundant (LEA) genes, we obtained a promoter similarity-based network that contained candidate genes that could plausibly complement the function of LEA genes. Importantly, 73.36% of 244 genes predicted by our method were experimentally confirmed to co-express with the LEA genes inmaturing rice embryos,making thismethodology a promising tool for biological systems analyses.

Original languageEnglish (US)
Pages (from-to)177-187
Number of pages11
JournalRice
Volume1
Issue number2
DOIs
StatePublished - Dec 1 2008

Keywords

  • Co-expression
  • Co-regulation
  • Transcription regulation

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Soil Science
  • Plant Science

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    Meier, S., Gehring, C., MacPherson, C. R., Kaur, M., Maqungo, M., Reuben, S., Muyanga, S., Shih, M. D., Wei, F. J., Wanchana, S., Mauleon, R., Radovanovic, A., Bruskiewich, R., Tanaka, T., Mohanty, B., Itoh, T., Wing, R., Gojobori, T., Sasaki, T., ... Bajic, V. B. (2008). The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network. Rice, 1(2), 177-187. https://doi.org/10.1007/s12284-008-9017-4