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Updated: Jul 29, 2025

Chromatin Immunoprecipitation Assay for Tissue-specific Genes using Early-stage Mouse Embryos
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Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development.

Fuqing Jiang1,2,3, Xin Zhou2, Yingying Qian1,4

  • 1Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

Nature Methods
|May 25, 2023
PubMed
Summary

Researchers developed a new method, microfluidic indexing-based spatial assay for transposase-accessible chromatin and RNA-sequencing (MISAR-seq), to map gene expression and chromatin accessibility in the developing mouse brain.

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Area of Science:

  • Neuroscience
  • Genomics
  • Molecular Biology

Background:

  • The brain's function depends on intricate anatomical and molecular organization.
  • Current molecular mapping of brain spatial organization is limited.
  • Understanding spatiotemporal gene regulation is crucial for developmental neuroscience.

Purpose of the Study:

  • To introduce MISAR-seq, a novel method for spatial profiling of chromatin accessibility and gene expression.
  • To investigate the spatial organization and regulatory logic of the developing mouse brain.

Main Methods:

  • Developed microfluidic indexing-based spatial assay for transposase-accessible chromatin and RNA-sequencing (MISAR-seq).
  • Applied MISAR-seq to profile chromatin accessibility and gene expression with spatial resolution.
  • Analyzed data from developing mouse brain tissue.

Main Results:

  • Successfully achieved spatially resolved joint profiling of chromatin accessibility and gene expression.
  • Generated molecular maps of the developing mouse brain.
  • Identified spatiotemporal regulatory patterns during development.

Conclusions:

  • MISAR-seq provides a powerful tool for high-resolution spatial multi-omics in complex tissues.
  • The study offers new insights into the regulatory mechanisms governing mouse brain development.
  • This method advances our understanding of brain development and spatial genomics.