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. 2015 Apr 6;212(4):539–553. doi: 10.1084/jem.20141380

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© 2015 Hatzi et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

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Figure 4. — BCL6 binding and gene regulation in Tfh cells differs compared with GC B cells with distinct pattern mainly outside promoters. (A) Overlap of BCL6-binding sites in Tfh (blue) and GC B cells (green). (B) Normalized BCL6 ChIP-seq read densities plotted for Tfh cells (y axis) versus B cells (x axis) for each peak corresponding to peaks common to Tfh and B cells, Tfh-only peaks, and B cell–only peaks. Density values were normalized to the total number of reads (rpm, reads per million). (C) Boxplots comparing BCL6 Tfh and GC B BCL6 ChIP-seq read densities for B cell–only peaks, Tfh-only peaks, and peaks common to Tfh and B cells. Density values were normalized to the total number of reads. (B and C) Input chromatin density was subtracted from each measurement. (D) Pie chart of the genome-wide distribution of BCL6 peaks common in GC B cells and GC Tfh cells based on RefSeq. Peaks occurring within ±2 kb of the TSS and TES were considered promoter and 3′UTR peaks, respectively. (E) BCL6 density tracks of BCL6 and PRDM1 loci that were commonly bound in GC Tfh and GC B cells. Read densities are shown in blue for GC Tfh BCL6 ChIP-seq and green for GC B BCL6 ChIP-seq. (F) Pie chart of the genome-wide distribution of GC B-only BCL6 peaks. (G) BCL6 density tracks of SYK and MSH6 that were bound by BCL6 in GC B cells but not in GC Tfh cells. (H) Pie chart of the genome-wide distribution of Tfh-only BCL6 peaks. (I) BCL6 density tracks the IL21 and PLCG1 loci that were bound by BCL6 in GC Tfh cells but not in GC B cells. (J) Tfh and GCB BCL6 read density on the SELPLG locus where BCL6 binds at different sites. ChIP-seq data are from two experiments, comprising primary CD4 T cells from three human donors. (K) qChIP experiments confirm BCL6 is selectively enriched at the SYK and IL21 loci in GC B and GC Tfh cells, respectively. BCL6 binds the PRDM1 promoter in both B and T cells. Nonspecific IgG antibody was used as a negative immunoprecipitation control. Data for cells from three separate donors are shown, representative of two independent experiments. Values are shown as percentage of input chromatin. The BCL6 intron 9 served as a negative control locus. Error bars indicate SEM.