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Many microscopy and genomics technologies that map chromatin proteins and modifications rely on the diffusion of antibodies (Abs) to target epitopes within whole nuclei. Here, we reveal a critical flaw in such methods that arises when Abs become trapped at the edge of nuclear structures and fail to reach internally positioned epitopes. This \u201cAb-trapping\u201d results in artifactual peripheral signal that fundamentally distorts the apparent positions of chromatin features across the genome and nucleus. Using computational modeling and experimental validation, we demonstrate that Ab-trapping is caused by a combination of three compounding factors\u2014high epitope abundance, high Ab affinity, and low Ab diffusion rates. Ab-trapping can thus systematically misrepresent the localization of many prevalent chromatin features like histone modifications, transcription factors, nucleolar proteins, and protein tags. We also show that this artifact manifests in multiple technologies, including immunofluorescence microscopy, more recent CUT&amp;Tag-seq, and likely any method relying on Ab diffusion. Finally, we outline readily implementable strategies to identify and mitigate Ab-trapping. Combined, our work presents a previously unrecognized yet prevalent artifact in Ab-based chromatin mapping methods and the means to resolve it.<\/jats:p>","DOI":"10.1093\/nar\/gkag615","type":"journal-article","created":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T11:20:00Z","timestamp":1780917600000},"source":"Crossref","is-referenced-by-count":1,"title":["Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7606-8381","authenticated-orcid":false,"given":"Konrad","family":"Chudzik","sequence":"first","affiliation":[{"name":"Max-Delbr\u00fcck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Chromatin (dys)function in disease group , Berlin, 10115 ,","place":["Germany"]},{"name":"RG Development & Disease, Max Planck Institute for Molecular Genetics , Berlin, 14195 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