  The binding of transcription factors (TFs) is essential for gene expression.
One important characteristic is the actual occupancy of a putative binding site
in the genome. In this study, we propose an analytical model to predict genomic
occupancy that incorporates the preferred target sequence of a TF in the form
of a position weight matrix (PWM), DNA accessibility data (in case of
eukaryotes), the number of TF molecules expected to be bound specifically to
the DNA and a parameter that modulates the specificity of the TF. Given actual
occupancy data in form of ChIP-seq profiles, we backwards inferred copy number
and specificity for five Drosophila TFs during early embryonic development:
Bicoid, Caudal, Giant, Hunchback and Kruppel. Our results suggest that these
TFs display thousands of molecules that are specifically bound to the DNA and
that, while Bicoid and Caudal display a higher specificity, the other three
transcription factors (Giant, Hunchback and Kruppel) display lower specificity
in their binding (despite having PWMs with higher information content). This
study gives further weight to earlier investigations into TF copy numbers that
suggest a significant proportion of molecules are not bound specifically to the
DNA.
