Transcription initiation occurs at an upstream alternative CGI promoter and not at the proximal promoters of MethExp genes. The evidence of transcriptional initiation based on CAGE tag intensity (log-transformed y-axis) is contrasted for three gene groups, MethExp (red), MethNotExp (green) and NotMethExp (blue) at (A) the proximal promoter and (B) the distal CGI (x-axis). C and D are analogous to A and B, respectively, for observed levels of transcription initiation based on Ser5-Pol II ChIP-seq intensity. For the pan-tissue pooled set of MethExp genes, the plot shows the CAGE signal (y-axis) at the (E) promoter and (F) associated distal CGIs of these genes when they are MethExp (yellow), MethNotExp (red), NotMethExp (green), and NotMethNotExp (gray) in other tissues (x-axis).
