csRNA-seq identifies active promoters and distal regulatory elements and their underlying transcription factor networks in a cell-type–specific manner. (A) Grouping of common and cell-type–specific csRNA-seq TSSs with DNase-seq and H3K27ac ChIP-seq across three different human cell lines (±1.5 kb to the TSS). (B) Known DNA motifs enriched in the distal regulatory elements of human K562, HCT116, and H9 embryonic stem cells identified using HOMER. Motif enrichment was calculated for sites located within (−150,+50) relative to TSSs for csRNA-seq or from (−100,+100) or (−500,+500) relative peak centers for DNase-seq and H3K27ac ChIP-seq, respectively. (C) TSSs identified by csRNA-seq provide a single-nucleotide anchor that facilitates accurate spatial analysis of DNA motifs compared with peaks as defined by DNase-seq or H3K27ac ChIP-seq.