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. 2023 Dec 4;56(1):100–111. doi: 10.1038/s41588-023-01603-8

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 1 — a, Representative genomic tracks showing RNAPII, BRG1, histone PTM occupancy by CUT&Tag, chromatin accessibility (RNAPII-S5P CUTAC), and transcriptional activity (START-seq) at the Nanog promoter and enhancer cluster and flanking genes. Previously annotated enhancer regions⁴¹ are shown on top. b, c, Heatmaps (bottom) and average plots (top) comparing RNAPII, BRG1, and histone PTM occupancy by CUT&Tag, relative to the primary peaks (summits) of RNAPII-S5P CUTAC (b) and RefSeq annotated gene TSSs (c), sorted by decreasing RNAPII-S5P occupancy. d, Violin plots of CUT&Tag signal distribution comparing RNAPII-S5P, BRG1, and histone PTM occupancies at specific set of gene promoters (TSS) showing RNAPII-S5P enrichment versus promoter-distal S5P CUTAC and pluripotency TF-binding peaks (Distal). Median value (solid line), upper and lower quartiles (broken lines) and outliers were calculated using the Tukey method. Numbers on top show mean values. e, Scatterplots comparing BRG1 and RNAPII S5P, S2P, and RPB3 CUT&Tag reads in 1,000 bp genome-wide consecutive non-overlapping bins. f, Heatmaps (bottom) and average plots (top) comparing chromatin accessibility (RNAPII-S5P CUTAC and ATAC-seq), nucleosome positions (MNase seq), and transcriptional activity (START-seq), relative to the primary peaks (summits) of RNAPII-S5P CUTAC; and RNAPII-S5P CUTAC signal relative to RefSeq annotated gene TSSs (extreme right). All datasets are representative of at least two biological replicates.