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We explored whether chromatin nanoscale packing domains are involved in stemness and response to chemotherapy. Using an optical spectroscopic nanosensing technology we show that ovarian cancer\u2010derived cancer stem cells (CSCs) display upregulation of nanoscale chromatin packing domains compared to non\u2010CSCs. Cleavage under targets and tagmentation (CUT&amp;Tag) sequencing with antibodies for repressive H3K27me3 and active H3K4me3 and H3K27ac marks mapped chromatin regions associated with differentially expressed genes. More poised genes marked by both H3K4me3 and H3K27me3 were identified in CSCs vs. non\u2010CSCs, supporting increased transcriptional plasticity of CSCs. Pathways related to Wnt signaling and cytokine\u2010cytokine receptor interaction were repressed in non\u2010CSCs, while retinol metabolism and antioxidant response were activated in CSCs. Comparative transcriptomic analyses showed higher intercellular transcriptional heterogeneity at baseline in CSCs. In response to cisplatin, genes with low baseline expression levels underwent the highest upregulation in CSCs, demonstrating transcriptional plasticity under stress. Epigenome targeting drugs downregulated chromatin packing domains and promoted cellular differentiation. A disruptor of telomeric silencing 1\u2010like (Dot1L) inhibitor blocked transcriptional plasticity, reversing stemness. These findings support that CSCs harbor upregulated chromatin packing domains, contributing to transcriptional and cell plasticity that epigenome modifiers can target.<\/jats:p>","DOI":"10.1002\/advs.202407426","type":"journal-article","created":{"date-parts":[[2025,3,11]],"date-time":"2025-03-11T17:19:04Z","timestamp":1741713544000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells"],"prefix":"10.1002","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3654-7350","authenticated-orcid":false,"given":"Yinu","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Obstetrics and Gynecology Northwestern University  Chicago IL 60611 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Frederick","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Northwestern University  Evanston IL 60208 USA"},{"name":"Center for Physical Genomics and Engineering Northwestern University  Evanston IL 60208 USA"},{"name":"Chemistry of Life Processes Institute Northwestern University  Evanston IL 60208 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karla Isabel","family":"Medina","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Northwestern University  Evanston IL 60208 USA"},{"name":"Center for Physical Genomics and Engineering Northwestern University  Evanston IL 60208 USA"},{"name":"Chemistry of Life Processes Institute Northwestern University  Evanston IL 60208 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth Thomas","family":"Bartom","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics Northwestern University  Chicago IL 60611 USA"},{"name":"Department of Preventive Medicine Northwestern University  Chicago IL 60611 USA"},{"name":"Robert H. 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