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. 2019 May 31;9:8140. doi: 10.1038/s41598-019-44597-2

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© The Author(s) 2019

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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Single molecule analysis of Dynlt1b and Xkr9 gene promoters using genome-wide NOMe-seq followed by NOMePlot in mESCs. (A,B) Population-averaged plots showing nucleosome occupancy (red, percentage of unmethylated GpCs) and DNA methylation (black, percentage of methylated CpGs) relative to the TSS (±500 bp) for transcriptionally active genes (n = 2512) (A) and DNA methylated silent genes (n = 1080) (B) in mESCs. Arrow indicates the direction of transcription. (C,D) Scatter plots with trendline showing population-averaged nucleosome occupancy (red) and DNA methylation (black) relative to the TSS of an active gene (Dynlt1b) (C) and a DNA methylated silent gene (Xkr9) (D). Nucleosome occupancy is calculated as the percentage of unmethylated GpC sites. DNA methylation is plotted as the percentage of methylated CpG dinucleotides. Arrow indicates the direction of transcription. (E,F) Lollipop diagram showing DNA methylation and nucleosome occupancy at the single molecule for Dynlt1b (E) and Xkr9 (F). Top panels show cytosine methylation at CpGs (white for unmethylated, black for methylated) and bottom panels show methylation patterns at GpC dinucleotides (white for unmethylated, blue for methylated). Red bars highlight GpC unmethylated regions long enough to accommodate a nucleosome. NDRs are marked with a grey box. Genomic coordinates of the analyzed regions are indicated.