Figure 6

TATA-TSS spacing is correlated with promoter and initiation site characteristics. (a-g) Sequence logos [43] for promoters divided into spacing subclasses based on the location of the most prominent TATA box. CAGE tag distribution trends in each spacing subclasses are shown below each logo; specifically, the median fraction of CAGE tags within each promoter for each spacing class is plotted using a log-scaled y-axis (see Materials and methods). The locations of the dominant TSS and the TATA-box start are indicated with black arrows. Both the initiation site (positions -3 to +1) consensus and CAGE tag distributions differ between the different classes. Of particular interest is the extended initiation site motif for promoters located at -33 and -34, as well as the different consensus for promoters with TATA boxes located at -28. The CAGE tag distribution is skewed in a direction that is consistent with alternative start sites at a more favorable spacing (closer to position -30 or -31). CAGE, cap analysis of gene expression; TSS, transcription start site.