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. 2012 Nov;22(11):2290–2301. doi: 10.1101/gr.139360.112

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© 2012, Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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Figure 3. — EP300 peaks that overlap H3K4me1-flanked regions have distinct properties. (A) Percent of EP300 peaks that directly overlap an annotated TSS (UCSC Genes; [dark green] peaks that overlap H3K4me1-flanked regions; [light green] peaks that do not overlap H3K4me1-flanked regions). Data for Heart (C57bl/6 mouse tissue taken at 8 wk), mES (Mouse ES-Bruce 4), and GM12878 generated by ENCODE and modENCODE consortia. (B) Average number ChIP-seq reads per peak for Pol2 (top row), H3K4me3 (middle row), and CTCF (bottom row) in a 2-kb window around the summits of indicated EP300 peaks (H3K4me1-flanked indicated by fl and dark green; non-H3K4me1-flanked, n-fl and light green). Three columns show data from the heart, mES, and GM12878, respectively. (C) EP300 ChIP-seq fold enrichment (determined by MACS) of EP300 peaks that overlap H3K4me1-flanked regions (fl; darker green), and EP300 peaks that do not overlap H3K4me1-flanked regions (n-fl; lighter green). Corresponding P-values calculated by two-tailed t-test. Numbers of peaks are as follows: melan-a fl, 2489; n-fl, 1133; heart fl, 3324; heart n-fl, 23,236; mES fl, 1258; mES n-fl, 20,062; GM12878 fl, 3404; and GM12878 n-fl, 6703.