Related Experiment Video
Updated: May 8, 2026
09:32
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
Published on: October 14, 2022
CoCUT&Tag maps linked chromatin states at single-molecule, single-cell resolution
Wenjie Sun1, Emma Baird1, Harry J Ashbaugh1
1Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
Biorxiv : the Preprint Server for Biology
|May 7, 2026
Summary
CoCUT&Tag enables single-cell measurement of dual chromatin features, revealing bivalent chromatin
Area of Science:
- Epigenetics and Genomics
- Single-cell analysis
- Chromatin regulation
Background:
- Profiling multiple chromatin features presents challenges in specificity, sensitivity, and co-occupancy analysis, especially in rare cell types.
- Bivalent chromatin, marked by H3K27me3 and H3K4 methylation, is hypothesized to maintain stem cell multipotency by poising developmental genes.
- Existing genomic methods have limitations in simultaneously assessing co-occurring epigenetic marks at single-cell resolution.
Purpose of the Study:
- To introduce CoCUT&Tag, a novel method for single-cell measurement of co-occurring chromatin features.
- To investigate the role of bivalent chromatin during human hematopoietic differentiation.
- To test the model that bivalent chromatin preserves stem cell multipotency and poises genes for activation.
Main Methods:
- Development of CoCUT&Tag utilizing synthetic antigen-peptide repeats and nanobodies to enhance Tn5 transposase targeting.
- Application of CoCUT&Tag for single-cell measurement of H3K27me3 and H3K4 methylation co-occupancy.
- Analysis of chromatin states and gene expression dynamics during human hematopoietic differentiation.
Main Results:
- Global bivalency increases during human hematopoietic differentiation, while active chromatin states are highest in stem and progenitor cells.
- Bivalent and unmarked genes exhibit similar activation timing but bivalent genes achieve higher expression with stronger enhancer association.
- Bivalent genes are preferentially derepressed upon loss of Polycomb-repressor proteins, indicating a distinct regulatory role.
Conclusions:
- Bivalent chromatin increases enhancer demand to facilitate high-amplitude gene activation.
- CoCUT&Tag effectively resolves questions regarding combinatorial chromatin regulation at single-cell resolution.
- The findings provide new insights into the regulatory mechanisms governing stem cell differentiation and gene poising.
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