W308 Next-Generation Genomics Tools for Reconstructing Transcriptional Networks in Eucalyptus

Date: Sunday, January 15, 2012
Time: 5:30 PM
Room: Sunrise
Steven G Hussey , Department of Genetics, University of Pretoria, Pretoria, South Africa
Eshchar Mizrachi , Department of Genetics, University of Pretoria, Pretoria, South Africa
Charles Hefer , Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria, South Africa
Andrew Groover , Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Davis, CA
Dave Berger , Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
Alexander Myburg , Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
Understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis in trees may facilitate effective approaches for improving wood properties. In Arabidopsis, the characterization of a highly interconnected transcriptional network regulating SCW biosynthesis has revealed the central importance of NAC (e.g. SND) and MYB transcription factors. Recent studies in Populus have uncovered conserved and unique components of the same transcriptional network in wood-forming tissues. It would be valuable to identify and compare the repertoire of gene targets regulated by SCW-related NAC and MYB homologs in the Eucalyptus grandis genome. Transcriptome and promoter::reporter analysis of transfected Arabidopsis mesophyll protoplasts have allowed for the identification of gene targets of Arabidopsis and Populus SCW transcription factors. Genome-wide identification of transcription factor targets in nontransgenic trees, however, requires efficient production and transfection of protoplasts derived from such trees. We are developing procedures for efficient preparation, transfection, inducible expression and transcriptome sequencing of E. grandis protoplasts to identify gene targets of SCW transcription factors. A complementary approach to identifying direct binding sites of transcription factors in planta is next-generation DNA sequencing of immunoprecipitated chromatin (ChIP-seq). Its application in plants is limited to herbaceous model species and no reports of ChIP-seq analysis in woody tissues currently exist. We are developing the application of ChIP-seq to E. grandis immature xylem. These techniques will allow us to rapidly characterize unknown transcription factors and discover novel cis regulatory elements involved in wood formation.