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. 2024 Apr 10;43(11):2166–2197. doi: 10.1038/s44318-024-00093-6

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024

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/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Karyoplot of CENP-A CUT&RUN peak density, representing the distribution of the CENP-A identified in control siNeg (blue track) and siDNAJC9 (red track) treated RPE1-Tet-GFP-CENP-A cells. Plot represents the average from two biological replicates for each condition. (B) Heatmap of genes (N = 9253) associated with peaks identified by CUT&RUN sequencing of CENP-A in control (siNeg) and DNAJC9-depleted cells in DOX-treated RPE1-Tet-GFP-CENP-A cells in two biological replicates. Read density (z-score normalized) for each condition is shown above the heatmap and centered on the midpoint of the CENP-A peaks identified in DNAJC9-depleted cells. (C) Pie chart representing the distribution of the 17,341 significant common peaks identified in DNAJC9-depleted CENP-A CUT&RUN datasets across the indicated genomic features. (D) Heatmap showing the fold change of significantly enriched CENP-A CUT&RUN peaks in DNAJC9-depleted cells compared to control cells (siNeg), calculated for genomic loci associated with various epigenetic marks. (E) Read density plot showing CENP-A CUT&RUN peaks identified in indicated conditions that overlap with peaks from ATAC-Seq experiments published previously (GSM6383021, (Zhang et al, 2023)). Plots are centered on the midpoint of the peaks identified. Source data are available online for this figure.