Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes

  1. Christopher H Bohrer
  2. Daniel R Larson  Is a corresponding author
  1. National Cancer Institute, United States


The role of the spatial organization of chromosomes in directing transcription remains an outstanding question in gene regulation. Here, we analyze two recent single-cell imaging methodologies applied across hundreds of genes to systematically analyze the contribution of chromosome conformation to transcriptional regulation. Those methodologies are: 1) single-cell chromatin tracing with super-resolution imaging in fixed cells; 2) high throughput labeling and imaging of nascent RNA in living cells. Specifically, we determine the contribution of physical distance to the coordination of transcriptional bursts. We find that individual genes adopt a constrained conformation and reposition toward the centroid of the surrounding chromatin upon activation. Leveraging the variability in distance inherent in single-cell imaging, we show that physical distance - but not genomic distance - between genes on individual chromosomes is the major factor driving co-bursting. By combining this analysis with live-cell imaging, we arrive at a corrected transcriptional correlation of ϕ ≈0.3 for genes separated by < 400 nm. We propose that this surprisingly large correlation represents a physical property of human chromosomes and establishes a benchmark for future experimental studies.

Data availability

The current manuscript is a computational study. Analysis code and modeling code are included in GitHub.

The following previously published data sets were used

Article and author information

Author details

  1. Christopher H Bohrer

    Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Daniel R Larson

    Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9253-3055


National Institutes of Health

  • Christopher H Bohrer

National Institutes of Health

  • Daniel R Larson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Robert H Singer, Albert Einstein College of Medicine, United States

Version history

  1. Preprint posted: July 8, 2022 (view preprint)
  2. Received: July 14, 2022
  3. Accepted: February 10, 2023
  4. Accepted Manuscript published: February 15, 2023 (version 1)
  5. Version of Record published: March 3, 2023 (version 2)


This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.


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  1. Christopher H Bohrer
  2. Daniel R Larson
Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes
eLife 12:e81861.

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