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Determining genome-wide transcription networks of TGA factors

PI: Jonathan Arias, University of Maryland, Baltimore County

Co-PI: Christopher Town, The Institute for Genomic Research

Funded by: NSF Arabidopsis 2010

The completed genome sequence of Arabidopsis thaliana codes for at least 1,533 transcriptional regulators, of which the majority are predicted to bind DNA. Interactions between these DNA-binding proteins and cognate promoter sequences are primary determinants in establishing spatial and temporal expression patterns of batteries of genes that effect homeostasis, development and adaptation. However, our present knowledge of target genes and regulatory networks for all but a few plant transcription factors remains rudimentary at best. Considering the challenge ahead, efforts to assign gene-regulatory functions to the relatively large number of uncharacterized transcription factors of this higher plant by 2010 will strongly benefit from more global and high-throughput approaches.

We use of a complementary and integrated strategy, involving hybridization of immunoprecipitated chromatin to whole-genome arrays (ChIP-chip) and gene expression analysis, for mapping transcriptional regulatory networks of Arabidopsis. Our paradigm for study is the TGA family of basic/leucine -zipper proteins, which comprise a complex transcriptional system with important regulatory functions in development and defense. Differences in DNA-binding properties within the 10-member Arabidopsis TGA transcription factor family in vivo suggest that they are likely to have both distinct and shared sets of target genes. A key question to be answered here is the identity of primary target genes and their associated networks.

To this end, cross-linked chromatin of salicylic acid-treated plants is isolated and immunoprecipitated with antibodies specific to individual TGA factors. After reversal of the cross-links, the DNA is PCR-amplified, labeled and hybridized to arrays.

Through this project, we have developed a promoter array (190,000 oligos) and a whole-genome array (1,126,000 oligos) that are currrently available from NimbleGen Systems, Inc. Sequences of the oligos and alignements to the genome are available here.

Description of the promoter and the whole-genome array