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. Author manuscript; available in PMC: 2017 Jul 21.
Published in final edited form as: Mol Cell. 2016 Jul 21;63(2):318–328. doi: 10.1016/j.molcel.2016.06.018

Figure 3. MLL1-dependent H3K4me2 marks PRE-like sequences in the human genome.

Figure 3

(A) Genome-browser track examples of H3K4me1/2/3 ChIP-seq +/- shMLL1 highlighting the loss of H3K4me2 at numerous CGIs near several homeodomain-containing genes. Green boxes represent CGIs. (B) Coverage profiles for H3K4me1/2/3, H3K27ac, and H3K27me3 +/- shMLL1. Heat maps are centered on H3K4me2 peaks and ranked by decreasing H3K4me2 signal at TSS-overlapping sites.1446 genes show significantly decreased H3K4me2 and increased H3K27me3 levels following MLL1 knockdown. Note the focused CTCF pattern at MLL1-dependent loci compared to 11916 other TSS. (C) Box plots quantifying histone modification levels shown in (B). P-values from two-sided student T-tests comparing occupancy +/- MLL1-RNAi are shown above plots. (D) Coverage profiles of histone modifications +/- shMLL at intergenic sites not overlapping with an annotated TSS. Note the association of H3K4me2 loss with regions of high CTCF occupancy. (E) Box plots quantifying data shown in (D). H3K4me2 is most significantly affected among the modifications considered. P-values, as calculated in (C) are displayed above plots.