Concentration-dependent transcriptional switching through a collective action of cis-elements

Abstract

Gene expression specificity of homeobox transcription factors has remained paradoxical. WUSCHEL activates and represses <i>CLAVATA3</i> transcription at lower and higher concentrations, respectively. We use computational modeling and experimental analysis to investigate the properties of the cis-regulatory module. We find that intrinsically each cis-element can only activate <i>CLAVATA3</i> at a higher WUSCHEL concentration. However, together, they repress <i>CLAVATA3</i> at higher WUSCHEL and activate only at lower WUSCHEL, showing that the concentration-dependent interactions among cis-elements regulate both activation and repression. Biochemical experiments show that two adjacent functional cis-elements bind WUSCHEL with higher affinity and dimerize at relatively lower levels. Moreover, increasing the distance between cis-elements prolongs WUSCHEL monomer binding window, resulting in higher <i>CLAVATA3</i> activation. Our work showing a constellation of optimally spaced cis-elements of defined affinities determining activation and repression thresholds in regulating <i>CLAVATA3</i> transcription provides a previously unknown mechanism of cofactor-independent regulation of transcription factor binding in mediating gene expression specificity.