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Updated: Jun 26, 2026
14:26
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
Light-based footprinting of a eukaryotic genome
Linnea Ögren1, Isabella Muylaert1, Kerryn Elliott1
1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden.
Science Advances
|June 24, 2026
Summary
Researchers developed Deam-seq, a new method to map protein-DNA interactions genome-wide in living cells. This technique uses UV light and sequencing to reveal where proteins bind DNA, advancing our understanding of genome regulation.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Understanding protein-DNA interactions is crucial for genome function.
- Studying these interactions in living cells is technically challenging.
- Existing methods like UV footprinting have limitations in scale.
Purpose of the Study:
- To introduce a novel genome-wide method for studying protein-DNA interactions in vivo.
- To enable high-resolution mapping of protein occupancy in unperturbed cells.
- To provide a scalable tool for analyzing protein-DNA binding dynamics.
Main Methods:
- Whole-genome deamination sequencing (Deam-seq) was developed.
- UV irradiation induces photoproducts (pyrimidine dimers) in DNA.
- Photoproducts are detected as mutations via sequencing, generating quantitative photofootprints.
Main Results:
- Deam-seq provides ultradeep coverage for quantitative photofootprints in yeast (Saccharomyces cerevisiae).
- The method resolves protein occupancy at high resolution without bias towards accessible DNA regions.
- Differential signals between cellular and naked DNA correlate with known regulatory sites and ChIP-seq data, indicating protective effects of DNA-binding proteins.
Conclusions:
- Deam-seq offers a powerful proof-of-concept for studying protein-DNA interactions using light and sequencing.
- This technique allows genome-scale analysis in the native cellular context.
- Deam-seq advances the study of genome regulation and function in vivo.
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