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. Author manuscript; available in PMC: 2019 Jan 6.
Published in final edited form as: Cell Rep. 2018 Nov 13;25(7):1898–1911.e5. doi: 10.1016/j.celrep.2018.10.061

Figure 4. Absolute per Cell-Normalized Chromatin Immunoprecipitation Reveals Global Effects of HMGN1 Overexpression on Histone Marks.

Figure 4.

(A) Metagene plots and read quantitation of H3K27ac and H3K4me3 ChIP-seq in Nalm6 cells stably expressing a doxycycline-inducible HMGN1 cDNA 6 hours after addition of doxycycline or vehicle to the culture medium. Plots on the left are relative median read count-normalized “traditional” ChIP-seq, and on the right, absolute per cell-normalized to sequencing reads from ChIP-seq of exogenous spiked-in Drosophila S2 cell nuclei. RPM, reads per million; nRPM, normalized reads per million; x axis of metagene plots shows the transcriptional start site (TSS) and 5 kb upstream and downstream. Boxplots represent the distribution of ChIP-seq peak height at each detected gene (compared by t test).

(B) Gene tracks showing a representative locus on chr17 where an increase in H3K27 acetylation after addition ofdoxycycline is only evident after applying per cell absolute spike-in normalization.

(C) Relative read counts of histone marks at peaks within 1 kb of the TSS of genes that significantly (fold-change >1.5, p < 0.05) increased (UP, red) or decreased (DOWN, blue) in expression after induction of HMGN1 overexpression. Distributions compared by t test.