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Chromosome conformation capture (Hi-C) has enabled genome-wide mapping of chromosomal folding, yet ensemble-averaged contact maps entangle biologically specific-folding interactions (SFIs) with nonspecific polymer compaction and mask single-cell heterogeneity. Here, we developed a polymer-based simulation framework in Escherichia coli to address these limitations. We found that a null model of 300\u2009000 random polymer configurations recapitulated the global chromosomal organization observed in Hi-C data, establishing that most Hi-C signals reflect generic polymer behavior in a confined volume. Contrasting null-model predictions with experimental Hi-C data isolated a small subset of SFIs (&amp;lt;7%) and generated a specific-fold ensemble of 20\u2009000 single-cell conformations that reproduced chromosomal interaction domains and single-cell heterogeneity. SFIs were enriched in the ter region, reduced nucleoid accessibility, colocalized with cryptic prophages, and depleted in positively supercoiled regions. H-NS and MatP emerged as major chromosome-wide and local determinants of SFIs, respectively. Furthermore, high-SFI regions correlated with stress-adaptive genes, whereas low-SFI regions harbored housekeeping genes. Together, our results established that a small number of biologically encoded SFIs superimposed on a polymer background shape the E. coli chromosome and gene expression, providing a quantitative framework for dissecting chromosome architecture and function.<\/jats:p>","DOI":"10.1093\/nar\/gkag979","type":"journal-article","created":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T06:38:49Z","timestamp":1792651129000},"source":"Crossref","is-referenced-by-count":0,"title":["Disentangling polymer confinement from specific-folding interactions reveals the drivers of\n                    <i>Escherichia coli<\/i>\n                    chromosome organization"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-8665-1020","authenticated-orcid":false,"given":"Pourya","family":"Delafrouz","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago , Chicago, IL 60607 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2688-2756","authenticated-orcid":false,"given":"Tanya","family":"Nesterova","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University , Baltimore, MD 21205 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7308-8619","authenticated-orcid":false,"given":"Frances E","family":"Harris","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University , Baltimore, MD 21205 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5691-298X","authenticated-orcid":false,"given":"Hammad","family":"Farooq","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago , Chicago, IL 60607 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8986-9812","authenticated-orcid":false,"given":"Lin","family":"Du","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago , Chicago, IL 60607 ,","place":["United 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Biophysical Chemistry, School of Medicine, Johns Hopkins University , Baltimore, MD 21205 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Liang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago , Chicago, IL 60607 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,22]]},"reference":[{"key":"2026102202384221900_B1","doi-asserted-by":"publisher","first-page":"102679","DOI":"10.1016\/j.sbi.2023.102679","article-title":"Insights in bacterial genome folding","volume":"82","author":"Y\u00e1\u00f1ez-Cuna","year":"2023","journal-title":"Curr Opin Struct 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