News & ViewsPublished: 13 November 2026Mapping transcriptionChenxu Zhu ORCID: orcid.org/0000-0003-4216-65621,2 Nature Structural & Molecular Biology (2026) Cite this articleView saved researchBinding of RNA polymerase to chromatin does not inherently indicate whether the polymerase is actively engaged in transcription. Integrating targeted chromatin-binding protein profiling with chemical labeling of single-stranded DNA can delineate transcription bubbles associated with RNA polymerase and other chromatin-bound proteins.This is a preview of subscription content, access via your institutionAccess options Access through your institutionAccess Nature and 54 other Nature Portfolio journalsGet Nature+, our best-value online-access subscription34.99 € / 30 days cancel any timeLearn moreSubscribe to this journalReceive 12 print issues and online access269.00 € per year only 22.42 € per issueLearn moreRent or buy this articlePrices vary by article type$1.95 to $39.95Learn morePrices may be subject to local taxes which are calculated during checkoutFig. 1: Linking protein occupancy to ssDNA with KAS-CUT&Tag.ReferencesVoss, T. C. & Hager, G. L. Nat. Rev. Genet. 15, 69–81 (2014).Article CAS PubMed Google Scholar Chappell, L., Russell, A. J. C. & Voet, T. Annu. Rev. Genomics Hum. Genet. 19, 15–41 (2018).Article CAS PubMed Google Scholar Wu, W., Greene, J. E., Ahmad, K. & Henikoff, S. Nat. Mol. Struct. Biol. https://doi.org/10.1038/s41594-026-01917-1 (2026).Article Google Scholar Barnes, C. O. et al. Mol. Cell 59, 258–269 (2015).Article CAS PubMed PubMed Central Google Scholar Wu, T., Lyu, R., You, Q. & He, C. Nat. Methods 17, 515–523 (2020).Article CAS PubMed PubMed Central Google Scholar Petermann, E., Lan, L. & Zou, L. Nat. Rev. Mol. Cell Biol. 23, 521–540 (2022).Article CAS PubMed Google Scholar Lyu, R. et al. Nat. Commun. 15, 6852 (2024).Article CAS PubMed PubMed Central Google Scholar Kim, S. H., Marinov, G. K. & Greenleaf, W. J. Genome Res. 35, 124–134 (2025).Article CAS PubMed PubMed Central Google Scholar Henikoff, S., Henikoff, J. G., Kaya-Okur, H. S. & Ahmad, K. eLife 9, e63274 (2020).Article CAS PubMed PubMed Central Google Scholar Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Science 339, 950–953 (2013).Article CAS PubMed PubMed Central Google Scholar Core, L. J., Waterfall, J. J. & Lis, J. T. Science 322, 1845–1848 (2008).Article CAS PubMed PubMed Central Google Scholar Download referencesAuthor informationAuthors and AffiliationsNew York Genome Center, New York, NY, USAChenxu ZhuDepartment of Systems and Computational Biomedicine, Weill Cornell Medicine, New York, NY, USAChenxu ZhuAuthorsChenxu ZhuView author publicationsSearch author on:PubMed Google ScholarCorresponding authorCorrespondence to Chenxu Zhu.Ethics declarationsCompeting interestsThe author declares no competing interests.Rights and permissionsReprints and permissionsAbout this article