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. 2020 Oct 9;11:5095. doi: 10.1038/s41467-020-18863-1

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© The Author(s) 2020

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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Fig. 1 — a Violin plots showing genome-wide distribution of biotin-labeled H3.3-SNAP⁹ in 5 kb windows, in mouse embryonic stem cells (ESC) and neuronal stem cells (NSC). Biotin labeling of H3.3-SNAP was performed at 0 h and followed over subsequent 3, 6, and 12 h⁹. Each datapoint is calculated as the log2 value of the mean coverage in each sample bin divided by the mean coverage value of its corresponding input sample bin. Data shown from n = 1 biological replicate. Source data are provided as a Source data file. b Genome tracks showing example region of time-ChIP⁹ in ESC showing overlap of H3.3-SNAP and endogenous H3.3²¹ with H3K27ac²⁰ at enhancers and H3K9me3⁷¹ at IAP ERVs. All tracks were normalized to Reads Per Genomic Content (RPGC). See also Supplementary Fig. 1 for controls and additional tracks. c Venn diagrams showing overlap of H3.3-SNAP 0 h⁹ peaks with endogenous H3.3 peaks in ESC²¹, H3K9me3⁷¹, and H3.3-SNAP 0 h peaks in NSC⁹. d Read density heatmaps and average profiles of H3.3-SNAP in ESC and NSC, at ESC H3.3 peaks²¹. Peaks were separated in two categories, H3.3-only and H3.3 + H3K9me3, according to coincidence with H3K9me3 peaks²¹. Overlap with 15 ChromHMM states³⁷, IAP ERV elements (from RepeatMasker) and H3.3-SNAP peaks in ESC and NSC is shown as additional heatmaps where the coincidence with a chromatin state or peak from the respective annotation set is indicated with a colored or black line. e Scatter plot showing relationship between H3.3²¹ and H3K9me3⁷¹ assessed over 5 kb bins genome-wide. Color scale represents density of underlying data points (5 kb bins). Bottom graph shows bins overlapping with IAP ERVs in black. Two-sided Wilcoxon rank sum (p < 2.2e⁻¹⁶) and Cohen’s effect size d (H3.3: 1.66 +/−0.04; H3K9me3: 2.91 ± 0.05) tests show significant enrichment for both at H3.3 and H3K9me3 in these 5 kb bins. Overlap with additional repeat families are shown in Supplementary Fig. 3. Source data are provided as a Source data file.