Additional file 9: Figure S5.
(A) Overlap between binding sites of condensin I-IDC, condensin II and SCC-2 is shown. Numbers under each factor indicate the total number of binding sites. Overlapping numbers are based on the number of SCC-2 peaks. Those binding sites that overlap with HOT regions are removed from this analysis. (B) The median SCC-2 ChIP signal is plotted over the TSS and TES of all annotated genes. SCC-2 ChIP signal is enriched at promoters, and is proportional to transcription. Genes were ranked into five groups (highest expressed, 1st quintile; lowest expressed, 5th quintile) based on RNA level. As a control, IgG ChIP signal was also plotted across the transcription start and end sites (panels below). (C) Top 200 autosomal SCC-2 sites were used for motif search with MDScan . The motif logo was created by web logo . This motif is present in 58% of the SCC-2 peaks. (D) Heat maps demonstrating ChIP enrichment across binding peak summits for condensin or SCC-2. The peaks are ordered from strongest (top) to weaker binding (bottom). Condensin I-IDC ChIP signal is high across all SCC-2 peak summits on the X (top left panel). By contrast, SCC-2 ChIP signal is high for the subset of strongest condensin I-IDC binding sites, which include the majority of condensin IDC recruitment sites (top right panel). The heat map indicates that condensin II is enriched at SCC-2 sites (bottom left panel) and SCC-2 is enriched at condensin II sites (bottom right panel). (E) Western blot analysis of SCC-2 amount in embryos used for quantitative ChIP (qChIP) (Figure 5G). The percent reduction in SCC-2 amount was calculated based on tubulin loading control and the control RNAi.
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Kranz et al. Genome Biology 2013 14:R112 doi:10.1186/gb-2013-14-10-r112