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. 2018 Mar 26;9:1226. doi: 10.1038/s41467-018-03538-9

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© The Author(s) 2018

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. 4 — Expansion of H3K27me3/H3K9me3 onto silenced genes in mDA neurons. a Genes repressed and H3K27me3-marked in both NPC and mDA gain H3K9me3 during terminal differentiation into mDA neurons: ChIP-seq heatmaps showing the abundance of H3K27me3, H3K4me3, and H3K9me3 as RPKMs ± 10 kb around TSS in NPC and mDA of silent (log2(RPKM + 1) < 1) and H3K27me3-marked genes in NPC. The arrow indicates a subset of silent and H3K27me3-marked genes displaying an increase in H3K9me3 in mDA compared to NPC. b Heatmap profiles of average H3K27me3, H3K4me3, and H3K9me3 RPKMs ± 10 kb around TSS of silent genes (log2(RPKM + 1) < 1) in NPC and mDA and categorized as K9/K27 or K4/K9/K27 in mDA. c Gene ontology (GO) of the top (−log10 (adj p-value), Fisher’s exact test) biological processes for silent genes (log2(RPKM + 1) < 1 in NPC and mDA neurons as in b that were K9/K27 or K4/K9/K27 in mDA neurons (n = 491). d Example of a silent and H3K27me3-marked gene in NPC that gains H3K9me3 in mDA: Left: UCSC Genome browser excerpt showing enrichment for H3K27me3 (gray, vertical scale 0–100 RPKM), H3K4me3 (red, vertical scale 0–160 RPKM), and H3K9me3 (blue, vertical scale 0–80 RPKM) within the Hoxa-locus. Right: Bars indicate average RPKM ± SD for Hoxa2, which is <1 in NPC and mDA