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Related Concept Videos

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Updated: May 16, 2025

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
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A Chemical Epigenetic Probe to Capture the Site-Specific DNA-Binding Protein Complex.

Jiajun Zhu1,2, Zhucui Li3, Dongxiang Xue1,2

  • 1Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA.

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|March 31, 2025
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Summary

The new Site-specific non-canonical amino acid resolved Protein EnRichment (SUPER) system captures proteins at specific DNA sites. This tool reveals key protein interactions regulating gene expression and cell fate decisions in human pluripotent stem cells.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Genomics

Background:

  • Site-specific DNA-protein interactions are crucial for gene regulation and cell fate.
  • Identifying these interactions at specific genomic locations like promoters and enhancers is technically challenging.
  • Understanding these interactions is key to deciphering gene regulatory networks.

Purpose of the Study:

  • To develop a novel chemical epigenetic tool for identifying site-specific DNA-binding proteins.
  • To investigate cell context-dependent DNA-protein interactions in human pluripotent stem cells (hPSCs).
  • To uncover novel genome regulators involved in maintaining pluripotency and directing cell differentiation.

Main Methods:

  • Development of the Site-specific non-canonical amino acid resolved Protein EnRichment (SUPER) system.
  • Incorporation of a photo-crosslinking amino acid into a nuclease-deficient dCas9 mutant.
  • Application of the SUPER system in hPSCs to capture and identify DNA-bound proteins at targeted genomic loci.

Main Results:

  • The SUPER system successfully captured proteins bound to specific genomic regions in hPSCs.
  • Identified the OCT4/SOX2/CARHSP1 complex binding the NANOG promoter, essential for pluripotency maintenance.
  • Revealed ZIC2 as a competitive inhibitor binding the NANOG promoter during ectoderm differentiation.
  • Discovered ZNF8 binding to an OCT4 regulatory region, crucial for maintaining naïve pluripotency.

Conclusions:

  • The SUPER system is a robust tool for uncovering site-specific genome regulators in a cell context-dependent manner.
  • SUPER provides valuable insights into gene regulatory networks that control cell fate transitions.
  • This technology facilitates the study of dynamic DNA-protein interactions in biological processes.