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. Author manuscript; available in PMC: 2014 Aug 8.
Published in final edited form as: Mol Cell. 2013 Aug 8;51(3):310–325. doi: 10.1016/j.molcel.2013.07.010

Figure 3. Relationship between eRNA expression and deposition of H4K5ac and H3K4me2.

Figure 3

(A) Hierarchical clustering and heat map of the fold change in eRNA and coding gene expression (eRNAs: RPKM>1, genes: FDR 0.01, RPKM>0.5). See also Figure S3A–S3D.

(B) Heat maps of normalized tag densities for GRO-Seq around 2 kb of de novo enhancers centered to nucleosome free regions as a function of time following KLA treatment.

(C) Temporal profile of H4K5ac normalized tag densities tag counts around 2 kb of de novo enhancers as a function of time following KLA treatment. See also Figure S3E–S3G.

(D) Distribution of GRO-Seq tags at around NFRs at de novo H3K4me2-associated enhancers as a function of time following KLA treatment.

(E) Temporal profile of change in H3K4me2-MNase ChIP-Seq tags at de novo enhancers following KLA treatment. See also Figure S3H.

(F) Coverage of H3K4me1 ChIP-Seq tags at de novo enhancers following LPS treatment (Ostuni et al., 2013).

(G) Heat map comparing the distribution of intergenic H3K4me1 and H3K4me2 regions and GRO-Seq signal. Pre-existing H3K4me2 regions centered to NFR are presented. See also Figure S3I.

(H) Comparison of GRO-Seq and H3K4me2 cumulative tag densities at enhancers characterized by exclusive unidirectional eRNA initiation from minus (left) or plus (strands). GRO-Seq signal is multiplied by ten compared to H3K4me2 signal.