{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Le MT"],"funding":["U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences","U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)","U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)","Schmidt Academy for Software Engineering - Office of the Provost, Caltech","U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development"],"pagination":["1752"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12914033"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["17(1)"],"pubmed_abstract":["Chromatin conformation is thought to be critical for enhancer function, but its dynamic, nanoscale organization is difficult to measure directly. Here we introduce PLOTTED (Probabilistic Localization of Oligopaint Tagged Target Element Distances), an integrated imaging and computational framework that infers chromatin architecture from targeted high-resolution imaging of cis-regulatory modules (CRMs). PLOTTED generates spatial distance distributions between DNA loci, enabling quantitative modeling of chromatin configurations across developmental time, spatial axes, and genotypes. Applying PLOTTED to the brinker locus in Drosophila embryos, we measured distances among three CRMs and used chromatin geometry as a proxy for regulatory activity. In wild type, CRM configurations shift dynamicall"],"journal":["Nature communications"],"pubmed_title":["Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization."],"pmcid":["PMC12914033"],"funding_grant_id":["R01HD106799","R35GM118146"],"pubmed_authors":["Le MT","Dunipace L","McGehee J","Stathopoulos A","Rumph D"],"additional_accession":[]},"is_claimable":false,"name":"Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization.","description":"Chromatin conformation is thought to be critical for enhancer function, but its dynamic, nanoscale organization is difficult to measure directly. Here we introduce PLOTTED (Probabilistic Localization of Oligopaint Tagged Target Element Distances), an integrated imaging and computational framework that infers chromatin architecture from targeted high-resolution imaging of cis-regulatory modules (CRMs). PLOTTED generates spatial distance distributions between DNA loci, enabling quantitative modeling of chromatin configurations across developmental time, spatial axes, and genotypes. Applying PLOTTED to the brinker locus in Drosophila embryos, we measured distances among three CRMs and used chromatin geometry as a proxy for regulatory activity. In wild type, CRM configurations shift dynamicall","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Jan","modification":"2026-07-16T06:51:03.262Z","creation":"2026-07-09T10:41:05.997Z"},"accession":"S-EPMC12914033","cross_references":{"pubmed":["41540049"],"doi":["10.1038/s41467-026-68460-x"]}}