Gene counts were computed by HTSeq (37) and used as input for edgeR 3.0.8 (38). Genes with Benjamini-Hochberg–adjusted P values less than 0.01 were considered to be differentially expressed, unless otherwise specified. RNA-seq heat maps adjacent to ChIP-seq heat maps display log2 fold change values of genes corresponding to TSSs nearest to ChIP-seq peaks and were displayed using Java TreeView (39). Gene Ontology functional analysis was carried out using Metascape with default parameters (40).

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