How affinity of the ELT-2 GATA factor binding to cis-acting regulatory sites controls C. elegans intestinal gene transcription

Abstract

We define a quantitative relation between the affinity with which the intestine-specific GATA factor ELT-2 binds to cis­ acting regulatory motifs and the resulting transcription of asp-1, a target gene representative of genes involved in C. elegans intestine differentiation. By establishing an experimental system that allows unknown parameters (e.g., the influence of chromatin) to effectively cancel out, we show that levels of asp-1 transcripts increase monotonically with increasing binding affinity of ELT-2 to variant promoter TGATAA sites. The shape of the response curve reveals that the product of the unbound ELT-2 concentration in vivo (i.e. [ELT-2 free] or ELT-2 “activity”) and the largest ELT-XXTGATAAXX association constant (Kmax) lies in the range of 5-10. We suggest that this (unitless) product (K*max[ELT-2 free] or the equivalent product for any other transcription factor) provides an important quantitative descriptor of transcription-factor/regulatory-motif interaction in development, evolution and genetic disease. A more complicated model than simple binding affinity is necessary to explain the fact that ELT-2 appears to discriminate in vivo against equal-affinity binding sites that contain AGATAA instead of TGATAA.