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Updated: Jan 20, 2026

Reusable Single Cell for Iterative Epigenomic Analyses
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CoBATCH for High-Throughput Single-Cell Epigenomic Profiling.

Qianhao Wang1, Haiqing Xiong1, Shanshan Ai1

  • 1Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.

Molecular Cell
|September 1, 2019
PubMed
Summary
This summary is machine-generated.

A new method called CoBATCH enables genome-wide mapping of single-cell protein-DNA interactions. This technique efficiently profiles chromatin-binding proteins in various tissues for detailed epigenetic analysis.

Keywords:
cell fate decisionchromatin stateendothelial cellsenhancerepigenomicssingle-cell ChIPsingle-cell analysis

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Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution
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Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • Genome-wide mapping of single-cell histone modifications and chromatin-binding proteins is challenging.
  • Existing methods lack efficiency and generalizability for diverse biological samples.

Purpose of the Study:

  • To develop a novel, efficient, and generalizable method for single-cell profiling of protein-DNA interactions.
  • To enable scalable, low-input epigenomic profiling in intact tissues and cell cultures.

Main Methods:

  • CoBATCH (combinatorial barcoding and targeted chromatin release) utilizes Protein A-Tn5 transposase fusion enriched by antibodies.
  • Tn5 transposase generates indexed chromatin fragments for library preparation and sequencing.
  • The method supports both native and cross-linked conditions for tens of thousands of single cells.

Main Results:

  • CoBATCH achieves efficient single-cell epigenomic profiling with low input requirements and minimal background noise (∼12,000 reads/cell).
  • Successful mapping of endothelial cell lineages across ten embryonic mouse organs.
  • Demonstrated deciphering of epigenetic heterogeneity and cis-regulatory mechanisms within cell populations.

Conclusions:

  • CoBATCH is a broadly applicable and easily deployable technology for single-cell protein-DNA interaction profiling.
  • The method obviates the need for specialized equipment, facilitating wider research adoption.
  • CoBATCH advances the understanding of cellular heterogeneity and epigenetic regulation at single-cell resolution.