An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

<div><p>Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3). However, standard ChIP-seq normalization and analysis methods fail to detect a decrease upon EZH2 inhibitor treatment. We overcome this challenge by employing an alternative normalization approach that is based on the addition of <i>Drosophila melanogaster</i> chromatin and a <i>D</i>. <i>melanogaster-</i>specific antibody into standard ChIP reactions. Specifically, the use of an antibody that exclusively recognizes the <i>D</i>. <i>melanogaster</i> histone variant H2Av enables precipitation of <i>D</i>. <i>melanogaster</i> chromatin as a minor fraction of the total ChIP DNA. The <i>D</i>. <i>melanogaster</i> ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 signal is now observed in ChIP-seq data from EZH2 inhibitor treated samples.</p></div

Reduced H3K27me3 binding is detected by ChIP-qPCR.

<p><b>(A)</b> ChIP was performed using chromatin from KARPAS-422 cells treated with the EZH2 inhibitor CPI-360. qPCR using the positive control primer <i>MYT1</i> showed reduced H3K27me3 occupancy in the presence of the inhibitor. <b>(B)</b> ChIP was performed using chromatin from PC9 cells treated with the EZH2 inhibitor GSK126. qPCR using the positive control primer <i>MYT1</i> showed reduced H3K27me3 occupancy in cells treated with the inhibitor. (<b>C</b>) Libraries were generated from KARPAS-422 cells using 15 cycles of PCR amplification. Library DNA was diluted and qPCR was performed using positive control primers for <i>MYT1</i> and <i>CCND2</i>. (<b>D</b>) Libraries were generated from PC9 cells as described in (C) and library DNA was used for qPCR using positive control primers for <i>MYT1</i> and <i>CCND2</i>. All experiments are represented as the mean of two independent experiments with qPCRs performed in triplicate ±SD. The <i>ACTB</i> promoter served as a negative control for all experiments.</p

EZH2 inhibition reduces global H3K27me3 levels, however standard ChIP-seq methods do not reveal the reduction.

<p><b>(A)</b> Western blot showing reduced global H3K27me3 levels in KARPAS-422 cells treated with 1.5 μM CPI-360 for 4 and 8 days. Whole cell extracts were resolved by SDS page and immuno-blotted with anti-H3K27me3. Anti-H3 immuno-blots show equal levels of total H3. <b>(B)</b> Western blot showing reduced global H3K27me3 levels in PC9 cells treated with 1 μM of GSK126 for 5 days. Whole cell extracts were resolved by SDS page and immuno-blotted with anti-H3K27me3. Anti-H3 immuno-blots show equal levels of total H3. <b>(C, D)</b> Representation of H3K27me3 ChIP-seq data using IGV. No obvious differences are detected in CPI-360 (C) and GSK126 (D) treated KARPAS-422 and PC9 cells when compared to vehicle-treated controls. <b>(E, F)</b> Genome-wide data from H3K27me3 ChIP-seq experiments under different treatment conditions are represented as scatter plots.</p

Schematic representation of the ChIP-seq spike-in protocol.

<p>ChIP-seq spike-in reactions are set up by adding the test chromatin of interest (human or other), the target antibody of interest, a small portion of <i>D</i>. <i>melanogaster</i> chromatin and the <i>D</i>. <i>melanogaster-</i>H2Av-specific antibody. The <i>D</i>. <i>melanogaster</i> spike-in chromatin is added in equal amounts and the H2Av antibody functions to pull down a small portion of the <i>D</i>. <i>melanogaster</i> chromatin in each reaction. After sequencing, tags are mapped to the genome corresponding to the test chromatin as well as to the <i>D</i>. <i>melanogaster</i> genome. The total number of tags uniquely mapping to the <i>D</i>. <i>melanogaster</i> genome are counted for each sample and used to generate correction factors (DMSO tags/inhibitor tags). The test chromatin tag counts are then normalized using the correction factors.</p

<i>D</i>. <i>melanogaster</i> tag counts from H3K27me3 ChIP-seq reactions are elevated in EZH2 inhibitor treated samples.

<p>H2Av bound regions of the <i>D</i>. <i>melanogaster</i> genome were determined using the H2Av antibody in ChIP-seq reactions containing <i>D</i>. <i>melanogaster</i> S2 or OSS chromatin. <i>D</i>. <i>melanogaster</i> tags from ChIP-seq spike-in reactions were mapped only to these pre-defined H2Av regions. <b>(A)</b> H3K27me3 ChIP-seq reactions with <i>D</i>. <i>melanogaster</i> spike-in in KARPAS-422 cells have a substantial increase in <i>D</i>. <i>melanogaster</i> tags in spike-in libraries prepared from CPI-360 treated cells both at 4 days and 8 days after treatment. <b>(B)</b> The increase was not observed in the control H3K9me3 reactions. <b>(C)</b> H3K27me3 ChIP-seq reactions with <i>D</i>. <i>melanogaster</i> spike-in in PC9 cells have a substantial increase in <i>D</i>. <i>melanogaster</i> tags in spike-in libraries prepared from GSK126 treated cells. <b>(D)</b> The substantial increase in tags was not observed in the control H3K4me3 ChIP-seq spike-in reactions.</p