csRNA-seq captured changes in the transcriptome with high fidelity. (A) Bone marrow–derived macrophages were isolated from C57Bl6 mice and stimulated with KLA (TLR4 agonist) for 1 h. (B) Comparison of transcriptional and epigenetic profiling methods at the mouse Acod1 locus in untreated (Ctrl) and activated (KLA) conditions after stimulation for 1 h with KLA. (C) Differentially expressed features in response to 1-h KLA as captured by RNA-seq and (D) csRNA-seq (348 vs. 20235 features at greater than twofold difference and <5% FDR). (E) DNA motifs enriched in KLA-induced regulatory regions compared with random, reduced, or unaltered regions (−150,+50 relative to TSSs). (F) Comparison of ATAC-seq, H3K27ac, and csRNA in capturing alterations is distal regulatory elements relative to changes in nearby gene transcription upon 1-h KLA stimulation. Scatter plots show the log₂ ratio of changes in activity upon KLA stimulation in distal regulatory elements relative to the change in gene expression of the nearest expressed gene as captured by GRO-seq.