Figure 5

Extended TATA-TSS distances require unambiguous PyPu initiation sites. The fraction of PyPu dinucleotides in a sliding 2 bp wide window was calculated for each TATA spacing class in the [-5, +5] promoter region. Promoters with extended TATA-TSS distances (32-34 bp) are depleted of PyPu dinucleotides immediately upstream of the dominant TSS [-1,+1] (namely, [-2,-1] and [-3,-2]; fraction of PyPu dinucleotides shown as grey bars) and have a PyPu consensus at this site. Introduction of PyPu dinucleotides in this region would probably create new TSSs with a more favored distance to the TATA box. The PyPu distribution is largely symmetrical in promoters where the TATA box is located at position -31 to -29, indicating a possible intrinsic stretching mechanism within the PIC for selecting strong initiation sites located further away than the most favored distance (30 or 31 bp). bp, base pairs; PIC, pre-initiation complex; Pu, purine; Py, pyrimidine; TSS, transcription start site.