Histone modification ChIP‐seq analysis

Methods for histone modification ChIP, library construction and sequencing, and processing of histone modification ChIP‐seq data, including the identification of peaks and enhancer regions, are described in Supplementary materials and methods.

CIC‐associated and IDH1‐associated differentially enriched (DER) peaks were identified using DESeq2, analogously to the identification of DE genes. DER peaks were required to meet a q‐value threshold of 0.05 and a fold‐change ≥ 2 to be considered significant, and additionally required directional concordance between both CIC‐KO replicate cell lines for CIC‐associated DER peaks. DER peaks were annotated with their associated genomic feature and nearest gene using ChIPseeker.

Enhancers were labelled as DER if an overlap was present with at least one H3K4me1 or H3K27ac DER peak. The nearest genes associated with DER enhancers were considered to be putative targets of such enhancers. De novo motif analysis was performed on downregulated and upregulated DER enhancers using HOMER, with the size parameter set to 500 bp as recommended for histone marked regions (http://homer.ucsd.edu/homer/ngs/peakMotifs.html) and otherwise default parameters.