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. 2017 Jan;27(1):15–26. doi: 10.1101/gr.210955.116

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© 2017 Lai and Pugh; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Figure 4. — Genomic DNA architecture of PICs. (A) Genomic sequences (100 bp in each row) surrounding TFIIB PIP-seq peaks (N = 8134) or their scrambled 100-bp counterparts were scanned with the YYANWYY (IUPAC nomenclature) (Smale and Baltimore 1989) consensus in a sliding window to calculate log-likelihood ratios (Stormo 2000). Rows for the PIC and scrambled sequence were then sorted independently of each other based on the average score in a 20-bp window that was centered on each TFIIB peak. (B) The top and bottom 25% of rows from panel A were used to generate composite plots. (C) Minor groove widths were calculated (Zhou et al. 2013) for the sequences defined in panel A and sorted based on panel A. (D) The top and bottom 25% of rows from panel C were used to generate composite plots. (E) TFIIB and Pol II PIP-seq tags were aligned and sorted based on panel A. (F) The top and bottom 25% of rows from panel E were used to generate composite plots. The initiation and pause regions are highlighted in gray and yellow, respectively.