Prior studies have indicated that expression driven by a promoter sequence can be successfully modeled
by describing the equilibrium binding of transcriptional activators and repressors to the promoter
sequences. The cooperative binding of these factors is also affected by transcriptional interference as
revealed in our earlier studies (A. Buetti‐Dinh et al, Molecular Systems Biology (2009) 5:300).
Transcriptional interference has been recognized as an important factor in the regulation of gene
expression due to the pervasive production of non‐coding RNAs during transcriptional initiation, which
then acts as a horizontal transmitter of information along the chromosome.
The expression due to the endogenous activator (Gal4p) is not determined only by its (cooperative)
binding to the DNA. Gal80 binds and blocks to the activator domain of Gal4, while Gal3 unblocks Gal4
when activated by galactose. Thus, the prediction of the effect of interference requires the
measurement and modeling of the cooperative binding of these proteins to Gal4p and in addition to the
modeling of the binding of Gal4p to DNA. Using proteomic approaches, we will start studying the
cooperative effects in the Gal4‐Gal80‐Gal3 protein‐protein interactions on gene expression.