Detection of basal mRNA transcription near binding sites for STAT1 and RNApolII. The binding of STAT1 in response to IFN-γ was compared with the binding of RNApolII and the transcription of mRNA in non-stimulated cells. Black line (ΔSTAT1): log2 of differential STAT1 binding in cells stimulated with IFN-γ. Green line (ΔRNApolII): log2 of differential RNApolII binding, relative to the average binding of RNApolII across the ENCODE region, in non-stimulated cells. Blue line (mRNA %max): percentage of maximum mRNA detection score across the window. Black boxes indicate the locations of exons; connecting lines indicate intronic regions; arrowheads within introns indicate the direction of transcription. (A) IRF1 gene and upstream region. (B) IFNaR1 gene. Raw data were obtained from Rozowsky et al' s tiling array analysis of STAT1 binding in response to IFN-γ , Bieda et al.'s tiling array of RNApolII binding in non-stimulated cells , and Sekinger et al.'s tiling array analysis of polyA RNA levels in non-stimulated cells .