{
  "abstract": "The three-dimensional organization of the bacterial chromosome is critical for gene regulation. 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 300 000 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 (<7%) and generated a specific-fold ensemble of 20 000 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.",
  "abstract_shown": true,
  "affiliations": [
    "Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago , Chicago, IL 60607 ,",
    "Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University , Baltimore, MD 21205 ,",
    "Department of Cell Biology, School of Medicine, Johns Hopkins University , Baltimore, MD 21205 ,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Pourya Delafrouz",
      "orcid": "0009-0000-8665-1020"
    },
    {
      "affs": [
        1
      ],
      "name": "Tanya Nesterova",
      "orcid": "0000-0002-2688-2756"
    },
    {
      "affs": [
        1
      ],
      "name": "Frances E Harris",
      "orcid": "0000-0002-7308-8619"
    },
    {
      "affs": [
        0
      ],
      "name": "Hammad Farooq",
      "orcid": "0000-0001-5691-298X"
    },
    {
      "affs": [
        0
      ],
      "name": "Lin Du",
      "orcid": "0009-0002-8986-9812"
    },
    {
      "affs": [
        2
      ],
      "name": "Jian Liu",
      "orcid": "0000-0003-2935-0349"
    },
    {
      "affs": [
        0
      ],
      "name": "Ao Ma",
      "orcid": "0000-0002-9872-7333"
    },
    {
      "affs": [
        1
      ],
      "name": "Jie Xiao",
      "orcid": "0000-0003-1433-5437"
    },
    {
      "affs": [
        0
      ],
      "name": "Jie Liang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fbgv2k0p6nk5d.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag979",
  "fulltext_url": "https://europepmc.org/articles/PMC13687565",
  "id": "fbgv2k0p6nk5d",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag979/8971829",
  "language": "eng",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7223175244",
  "pdf_url": "https://academic.oup.com/nar/article-pdf/54/19/gkag979/72302036/gkag979.pdf",
  "pmcid": "PMC13687565",
  "pmid": "42908400",
  "published": "2026-10-01",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/fbgv2k0p6nk5d.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag979",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag979/8971829"
    },
    {
      "first_seen": "2026-10-30T12:19:57Z",
      "native_id": "MED:42908400",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42908400"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Chromatin Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Disentangling polymer confinement from specific-folding interactions reveals the drivers of Escherichia coli chromosome organization",
  "title_text": "Disentangling polymer confinement from specific-folding interactions reveals the drivers of Escherichia coli chromosome organization",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:57Z",
  "url": "https://research.draconitic.com/paper/fbgv2k0p6nk5d",
  "venue": "Nucleic Acids Research",
  "versions": []
}