V-plots reveal chromatin features of transcription factor binding sites. (a) V-plot of MNase-seq data from Kent et al.  centered on binding sites for the Cbf1 transcription factor. Figure adapted from Henikoff et al. . (b) Interpretive diagram of a V-plot. A dot representing the midpoint of each paired-end fragment is placed on the graph. Its Y-axis value represents its length and its X-axis value represents the distance of its midpoint from the center of a given genomic feature (in this case, a transcription factor binding site (TFBS)). Locations of dots corresponding to each fragment are indicated by red arrows. The minimal region protected by the transcription factor (TF) is indicated by the intersection of the left and right diagonals on the Y-axis and also as the width of the gap on the X-axis resulting from extrapolation of the diagonals to Y = 0. The left diagonal results from fragments cleaved precisely to the right of the TF-protected region, and the converse is true of the right diagonal. The triangular densities flanking the TF-protected region are generated by protected regions adjacent to the TFBS that are cleaved between the TFBS and the protein responsible for the density.
Zentner and Henikoff Genome Biology 2012 13:250 doi:10.1186/gb-2012-13-10-250