Nodal/Activin Signaling in ES Cell Fate Decisions Figure 4. Phospho-Smad2 Binding to the Global ES Cell Genome Changes Dynamically in a Dose-Dependent Manner. (A) Proportional Venn diagram of overlapping and treatment specific pSmad2 binding peaks identified by ChIP-Seq from same passage ES cells cultured for 18 hours in Activin (ACT), DMSO control or SB in KSR media. Overlaps were defined using genomic coordinates of the start and end of peak positions identified with the MACS program using the same parameters for each treatment. Total numbers of peaks are stated for each condition and percentage of peaks in each Venn diagram segment is indicated in parentheses. (B) Graph showing frequency of pSmad2 peaks with respect to distribution in the indicated genomic locations including the transcriptional start sites (TSS) and transcriptional termination sites (TTS) relative to mouse RefSeq genes. Frequency is expressed as percentage of all pSmad2 binding peaks in conditions of high (Activin), medium (DMSO) and low (SB) signaling. (C) High resolution view of pSmad2 binding frequency within +/22 kb of the TSS of target genes. Genomic distance is expressed in base pairs (bp) upstream (negative) and downstream (positive) of the TSS while frequency is shown as percentage of pSmad2 binding peaks binned in 50 bp intervals out of the total number of peaks for each treatment. doi:10.1371/journal.pgen.1002130.g004 PLoS Genetics | www.plosgenetics.org 9 June 2011 | Volume 7 | Issue 6 | e1002130