Extended Data Fig. 1: Chromatin regulation of integrated regulatory elements.
From: CRISPR–ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia
a) ChIP-qPCR analysis of H3K27ac ChIP performed in parental K562 cells or K562 cells infected with the CRISPR-ChIP plasmid containing an EF1a promoter. Primers for a negative control region (Neg Ctrl), endogenous EF1a or regions spanning the gRNA/EF1a (Primer 1), and EF1a/Puro (Primer 2) within the lentiviral CRISPR-ChIP vector were used, data represents mean +/− SD from three independent biological replicates. b) ChIP-qPCR analysis of H3K27ac, H3K4me3, H3K9ac and RNA-Pol II ChIP at the endogenous PGK promoter or integrated PGK promoter-Puro reporter, an intergenic region not enriched in active histone marks was used as a negative control (Neg control). Data represents mean +/− SD from three independent biological replicates. c) ChIP-qPCR analysis of H3K27ac, H3K4me3, H3K79me2 and RNA-Pol II ChIP at the endogenous MEIS1 promoter or integrated MEIS1 promoter (~1.2Kb upstream of TSS)-Puro reporter, an intergenic region not enriched in active histone marks was used as a negative control (Neg control). Data represents the mean from two independent biological replicates. d) ChIP-qPCR analysis of H3K27ac, H3K4me3, and H3K9ac ChIP at the endogenous MYC enhancer or integrated MYC enhancer-mCMV-Puro sequence, an intergenic region not enriched in active histone marks was used as a negative control (Neg control). Data represents the mean from two independent biological replicates. e) ChIP-qPCR analysis of H3K79me2 in K562 cells infected with the CRISPR-ChIP plasmid and treated with DOT1L inhibitor (SGC0946) for 9 days. Primers for Negative control region (Neg Ctrl), Meis1, EF1a, and a region spanning the gRNA/EF1a were used, data represents mean +/− SD from three independent biological replicates. f) qPCR analysis of H3K27ac ChIP in K562 cells infected with the CRISPR-ChIP vector and treated with either DMSO or CBP/P300 inhibitor (A-485) for 24hrs. Primers for Negative control region (Neg Ctrl), Meis1, EF1a, and a region spanning the gRNA/EF1a were used, data represents the mean from two independent biological replicates. g) NGS representation of control sgRNAs at day 2, day 10, ChIP input day 10, and H3K79me2 ChIP (Left panel). NGS representation of DOT1L sgRNAs at day 2, day 10, ChIP input day 10, and H3K79me2 ChIP (Right panel).
