Distribution of the TFIIB/TBP/Pol II in CpG islands that overlap mRNA TSSs.

(A) Peak-pair distribution for TFIIB, TBP and Pol II at the 5,095 CpG islands that overlap with the 6,511 mRNA TSSs from Fig 1B (78% overlap), and with the direction of transcription to the right. Rows are linked, and sorted by CpG island length. CpG island left and right borders are indicated by blue and red bars, respectively. (B) Shown is the averaged data from panel A. (C) TFIIB locations were sorted by location, and inter-TFIIB distances calculated (red trace). Data were then sorted by distance, and the standard deviation of TFIIB occupancy was calculated on a sliding window of 30 values. Peak calling parameters preclude detection of two separate TFIIB locations <~40 bp apart. Those that were 40–70 bp apart were correlated, whereas those >~70 bp apart were uncorrelated.