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. Author manuscript; available in PMC: 2017 Oct 20.
Published in final edited form as: Mol Cell. 2016 Oct 20;64(2):347–361. doi: 10.1016/j.molcel.2016.09.026

Figure 2. H3S28 phosphorylation is targeted to lineage-specific and stimulation-responsive chromatin.

Figure 2

(A–B) H3S28ph ChIPseq (0′, 30′ - peak of signal) and RNAseq (0′, 60′) profiles in LPS-stimulated bone marrow derived macrophages for (A) constitutively expressed genes, Tubb5 and Rps2, and (B) LPS-induced Ifnb1, Il27, Cxcl10, Tnf, Il12a (also with 120′ RNAseq) with y-axis scale (tag density) indicated.

(C) All genes were ranked by H3S28ph signal density (RPM) at their TSS+/− 2kb. A threshold for the top H3S28ph genes, purple, was empirically determined based on ChIPseq signal over background (RPM>1.83).

(D) Fold change in mRNA following LPS treatment for all genes (gray) or top H3S28ph genes (purple, RPM>1.83). p<0.0001, Student’s t-test.

(E) Heat map displaying p-values of highly enriched transcription factor (TF) motifs from three categories: general (control) TFs (left), environmental response TFs (middle), macrophage lineage specifying TFs (right), for H3S28ph-positive (overlap of p300 and H3S28ph enriched regions) and –negative (p300 enriched sites lacking H3S28ph enrichment) enhancers. Enhancer coordinates were analyzed with Pscan-ChIP (see methods).

(F) H3S28ph ChIPseq signal (RPM) around the TSS (+/− 2kb) of genes that are not expressed (n.e.), primary response genes (PRG), MAPK-dependent genes, and NF-κB-dependent genes (NF-κB). Gene lists derived from Tong et al., 2016. Mean, std dev., 95% CI, with p<0.01 (**) and p<0.05 (*), Student’s t-test.

See also Figure S2.