Fig. 4.

V-plot of the Abf1 transcription factor. (A) Map of the 400-bp region spanning Abf1 transcription-factor binding sites is shown, where data are combined for the 2.5- and 20-min time points (Upper, blue), and differentially colored (Lower, red for 2.5 min and green for 20 min). Orientation is based on alignment with the Abf1 consensus motif. (B) Schematic diagram illustrates how the map is interpreted. Fragments are indicated below the graph. A fragment that spans a protected region (first blue fragment) results in a dot placed in the central sector (vertical red arrow). The left diagonal results from fragments cleaved precisely on the right side of the protected region (second blue fragment), and likewise for the right diagonal. The minimal protected region is at the intersection of the diagonals on the y axis, and is also represented as the width of the gap on the x axis (extrapolation of the diagonal red lines to y = 0), which in the case of Abf1 is 20 bp. The open box represents a fragment that is not observed because its left end is protected from cleavage. The flanking triangle densities are produced by protected fragments that are near or adjacent to Abf1 but are cleaved in between.