Figure 2

Distribution of ChIP-seq peaks within the genome. A. PU.1 and Spi-B have similar binding patterns in relation to features in the genome. B. Profiles and associated heatmaps of ChIP-signal at the transcriptional start site of Mouse RefSeq genes. Profiles represent the regions of strongest binding, which are clustered around the transcriptional start site. C. All clusters of PU.1 and Spi-B signal in relation to mouse RefSeq genes. Five different patterns of binding were observed, where the largest cluster contained genes without transcription factor binding at the promoter. Clusters 2 and 3 contained genes with binding upstream or downstream of the promoter, although Spi-B binding was often seen at the transcription start site. Cluster 4 contained regions with the highest log2 signal. Cluster 5 was gene with a broad region of transcription factor binding at the TSS. Top row shows results from anti-FLAG ChIP-seq of 3XFLAG-PU.1 in WEHI-279 cells, second row shows results from anti-FLAG ChIP-seq of Spi-B in WEHI-279 cells, and third row shows results from anti-PU.1 ChIP-seq in mouse splenic B cells (GSE21512). D. Profile of DNase genomic footprinting (DGF) at regions of significant ChIP enrichment for PU.1 and Spi-B. Regions of PU.1 or Spi-B binding demonstrated increased DNase sensitivity compared to regions outside the peaks. E. Profile of RNA Polymerase II ChIP-signal in B cells at regions of ChIP enrichment for PU.1 and Spi-B. PolII data confirmed that significant PU.1 and Spi-B peaks frequently occur at sites of transcription initiation. F. Profile of the chromatin feature H3K36me3, a marker of heterochromatin and gene bodies, at peak regions for PU.1 and Spi-B.