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. 2022 Aug;32(8):1529–1541. doi: 10.1101/gr.276766.122

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© 2022 Hansen and Hodges; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 4. — Regulatory regions deﬁned by ATAC-STARR exhibit annotations, histone modiﬁcations, and TFs characteristic of their function. (A) Annotation of regulatory regions relative to the transcriptional start site (TSS). The promoter is deﬁned as 2 kb upstream and 1 kb downstream of the TSS. (B) Annotation of regulatory regions by the ChromHMM 18-state model for GM12878 cells. (C) Heat maps of GM12878 ENCODE ChIP-seq signal and regulatory activity for proximal and distal ATAC-STARR-deﬁned regulatory regions. Proximal regions were classiﬁed as within 2 kb upstream and 1 kb downstream of a TSS; all other regions were annotated as distal. Active and silent regions were ranked by mean activity signal for both proximal and distal regions. (D,E) Transcription factor motif enrichment analysis as quantiﬁed by HOMER. Fold-change values are relative to the default background calculated by HOMER.