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Figure 2 | BMC Genomics

Figure 2

From: Relationship between estrogen receptor α location and gene induction reveals the importance of downstream sites and cofactors

Figure 2

Characteristics of weak and strong ChIP sites. A. Average nucleotide composition profile for ChIP sites with ERE consensus sites (posterior probability > 0.5). The sequences are centered on the ERE. Both sets, the low (left panel) and high (right panel) stringency sites, show a maximum GC enrichment within 200 bp of the ERE. Notice that GC content has not reached genome wide baseline at +/- 2.5 kbp, and drop-off is faster for the stronger sites (right). Each gray dot represents the mean frequency at one position, smoothed mean (black) +/- 2SD (gray) and shown as lines. B. Localization of hERα binding sites relative to annotated transcription start sites (TSSs) and poly-adenylation sites (PASs). The percentage of occurrence is calculated relative to the number of sites in the full window (± 50 kbp of TSS or of PAS, bin size 500 bp). Coordinates are taken positive in the transcript direction but results show absence of directionality in the profiles. Left panel: Distribution of distances from TSSs for sites with 10<t<16 mapped in the 5' regions. The noticeable peak around the TSS covers 12% of the total number of sites in the region. We thus find a tight colocalization with the TSS (defined as 0, green profile) for a subset of sites. In contrast, no colocalization is evident for the PAS (red profile). Right panel: Distribution of distances from TSSs for sites with t>16 mapped in the 5' regions. In this case, sites are uniformly distributed in the 50 kbp around the TSS (green profile) and around the PAS (red profile).

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