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. 2022 Dec 27;12:22425. doi: 10.1038/s41598-022-23614-x

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© The Author(s) 2022

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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CHD8 and ELK1 cooperate to regulate chromatin accessibility. (a) Normalized CHD8 signal and ATAC-seq signal in CHD8-KO and the control samples plotted, and ELK1 motif density plotted as a green enrichment plot. Genome-wide ChIP-seq and ATAC-seq signal divided into three groups: sites with exclusive enrichment for ELK1 motif, sites without ELK1 motif, and the control sites, which are the randomly shuffled peak sets from control samples. For each group, we compared the ATAC signal from KO to the control sample. (b) Cross-correlation analysis of ATAC-seq signal with NucleoATAC to measure nucleosome density. The enrichment plot is a subset of the calculated nucleosome density signal taken from TSS with ± ELK1 (ETS) motif (motif occurrence > 1). (c) Violin plots compare normalized and averaged nucleosome density signal at 100 bp region around the position + 1 of TSS with the presence or absence of ELK1 motif. Statistical analysis of distribution comparison is calculated with the Kolmogorov Smirnov test. (d) CHD8 binding signal taken from 100 bp upstream and downstream of transcription start sites (TSS), with the presence or absence of ELK1 motif.