Combinatorial Regulation of Gene Expression in the Vascular Cambium of Populus trichocarpa

In this talk, we present transcriptional regulatory models describing the complex interdependencies between transcription factors and their target genes during secondary growth and wood formation in Populus trichocarpa. Transcription factors bind cis-regulatory elements to regulate gene expression by either activating or suppressing transcription. Transcription factors commonly work in combinatorial fashion to integrate developmental, physiological or environmental response processes. Examples of combinatorial regulation by transcription factors include dimerization, direct interactions in protein complexes, and indirect genetic or epigenetic interactions. We integrated results from transcription factor binding (ChIP-seq) and expression (RNA-seq) experiments for three homeobox transcription factors that play fundamental roles in vascular cambium regulation, ptBELLRINGER, ARBORKNOX1 and ARBORKOX2. Genome-wide binding patterns are described for each transcription factor, including instances of genes that are co-bound by two or more of the transcription factors. Single and combinatorial binding patterns are contrasted with regards to their locations relative to genes, their different effects on gene expression. Furthermore, we apply association rule techniques, commonly used in market basket analysis, to identify frequently occurring combinations of transcription factors associated with vascular cambium expression. Together, this integrated approach increases the specificity of regulatory models and identifies transcription factor combinations relevant to the regulation of the vascular cambium and wood development.