IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-22189-x.html
   My bibliography  Save this article

Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales

Author

Listed:
  • Joris J. B. Messelink

    (Ludwig Maximilian University Munich)

  • Muriel C. F. Teeseling

    (University of Marburg
    Friedrich Schiller University Jena)

  • Jacqueline Janssen

    (Ludwig Maximilian University Munich)

  • Martin Thanbichler

    (University of Marburg
    Max Planck Institute for Terrestrial Microbiology
    Center for Synthetic Microbiology (SYNMIKRO))

  • Chase P. Broedersz

    (Ludwig Maximilian University Munich
    Vrije Universiteit Amsterdam)

Abstract

The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi–C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.

Suggested Citation

  • Joris J. B. Messelink & Muriel C. F. Teeseling & Jacqueline Janssen & Martin Thanbichler & Chase P. Broedersz, 2021. "Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22189-x
    DOI: 10.1038/s41467-021-22189-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-22189-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-021-22189-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Janni Harju & Muriel C. F. Teeseling & Chase P. Broedersz, 2024. "Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22189-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.