Synthetic deconvolution of an auxin-dependent transcriptional code

Most transcription factors (TFs) specifically bind small DNA sequences that are too frequent in the genome to explain the specificity of genes expression. Here we studied how TF-DNA interplay codes gene patterning using a reductionist approach centered on the study of ARFs multigenic family of TF in plants, involved in the transcriptional responses to auxin hormone, and their preferential DNA binding sites. Our study decorticated the diversity of ARFs binding and regulatory properties on different cis-elements and uncovered a feedback from DNA to TF as ARF regulatory properties are not intrinsic to the ARF but depend on the cis-elements they bind. We show that in vivo this two-layers regulatory code and the combinatorial effects of both TF and cis-elements permit to generate a wide array of expression patterns at the organ scale. This work makes one step further in understanding the "binding paradox" of TFs and the cis-regulatory code. Single cell RNAseq approach on Arabidopsis thaliana, 7day old seedling, cultivated in vitro, MS/2, sucrose 1%, Agar 1%, and treated with IAA 1 μM for 16 h or Mock. Experiment was performed on 4 lines carrying the DR5, ER13, DR15 or IR8 synthetic promoters followed by a mTurquoise reporter.