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Related Concept Videos

Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

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Related Experiment Video

Updated: May 8, 2026

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
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
PubMed
Summary

CoCUT&Tag enables single-cell measurement of dual chromatin features, revealing bivalent chromatin

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Last Updated: May 8, 2026

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

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.