Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana

Abstract

Our knowledge of the genetic control of wood formation (i.e., secondary growth) is limited. Here, we present a novel approach to unraveling the gene network regulating secondary xylem development in Arabidopsis, which incorporates complementary platforms of comparative-transcriptome analyses such as “digital northern” and “digital in situ” analysis. This approach effectively eliminated any genes that are expressed in either non-stem tissues/organs (“digital northern”) or phloem and non-vascular regions (“digital in situ”), thereby identifying 52 genes that are upregulated only in the xylem cells of secondary growth tissues as “core xylem gene set”. The proteins encoded by this gene set participate in signal transduction, transcriptional regulation, cell wall metabolism, and unknown functions. Five of the seven signal transduction-related genes represented in the core xylem gene set encode the essential components of ROP (Rho-related GTPase from plants) signaling cascade. Furthermore, the analysis of promoter sequences of the core xylem gene set identified a novel cis-regulatory element, ACAAAGAA. The functional significances of this gene set were verified by several independent experimental and bioinformatics methods.

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Acknowledgments

We thank John Ohrlogge at Michigan State University for the stem epidermis GeneChip data, and NASCArrays for various Affymetrix GeneChip data. This work was supported by the USDA CSREES (grant no. 01-34158-11222 and 2002-34158-11914 to K.H.H), the National Science Foundation (grant no. IBN-0131386 to E.P.B) and the Department of Energy (grant no. DE-FG02-04ER15627 to E.P.B).

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Correspondence to Kyung-Hwan Han.

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Communicated by K. Shirasu.

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Ko, J., Beers, E.P. & Han, K. Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana . Mol Genet Genomics 276, 517–531 (2006). https://doi.org/10.1007/s00438-006-0157-1

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Keywords

  • Arabidopsis
  • Comparative transcriptome analysis
  • Genechip
  • Secondary cell wall
  • Secondary xylem
  • Wood formation