Transcriptional regulation of cell-type specific gene expression in the Arabidopsis root

Identifying and characterizing transcription factor binding specificities in DNA sequence is crucial for understanding how gene expression is regulated across the genome. A more comprehensive understanding of this process could have benefits in synthetic promoter applications and the design of genetically modified organisms. In this study, promoter DNA for genes exhibiting cell-type specific expression in the Arabidopsis root are analyzed to identify distinct regulator motifs implicated in directing cell-type specific gene expression. A combination of de novo motif prediction and a priori mapping of known cis regulatory motifs from publically available data identifies multiple motif candidates significantly enriched in the promoter sequences of co-expressed genes specific for epidermal, cortex and endodermal expression. Several putative endodermal specific motifs are further analyzed for positional biases and in planta expression. Results show that different cell-types contain statistically significant enrichments of both predicted and known cis-regulatory motifs. These results will help future research in designing synthetic promoters for directing the cell-type specific expression of trans-genes.