Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes
Abstract
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. https://github.com/CHB-Bohrer/co-bursting
Article and author information
Author details
Funding
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
- Robert H Singer, Albert Einstein College of Medicine, United States
Publication history
- Preprint posted: July 8, 2022 (view preprint)
- Received: July 14, 2022
- Accepted: February 10, 2023
- Accepted Manuscript published: February 15, 2023 (version 1)
- Version of Record published: March 3, 2023 (version 2)
Copyright
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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