Figure 3

Insights into transcription factor binding. (A) Examples of a consistent increase in read depth at a single position, indicating that exonuclease digestion is blocked at this position. (The corresponding drop in read depth is simply a reflection of the 36-nucleotide reads from the sequencer.) The corresponding peaks from ChIP-seq are also shown for the FoxA1 examples. (B) A random sample of positions in the genome, 100 on the top strand and 100 on the bottom strand, at which the read depth increases by at least 100 reads on the top and bottom strands, respectively. The vertical line indicates the position of the increase in read depth. The red and blue lines indicate the position of top- and bottom-strand forkhead motifs, with a strong pattern of motifs exactly 9 bp downstream from the increase in read depth. The plot shows a window of 100 bp centred on the increase. The density plots below show the density of top (red) and bottom (blue) strand motifs across the window. (C) An example of paired mesas on the top and bottom strand, with overlapping motifs in a palindromic orientation. The 33 bp distance between the top- and bottom-strand mesa edges is the most common distance.