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Related Experiment Video

Updated: Aug 19, 2025

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
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3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells.

Karolina Jodkowska1,2,3, Vera Pancaldi4,5, Maria Rigau4,6,7

  • 1DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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Summary

Replicative stress activates dormant DNA replication origins in mammalian cells. Origin efficiency correlates with proximity to gene start sites and chromatin interactions, suggesting organization into replication factories.

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Area of Science:

  • Cell Biology
  • Genetics
  • Molecular Biology

Background:

  • DNA replication initiates at numerous origins in mammalian cells.
  • Dormant origins can be activated by replicative stress, but their regulation is unclear.

Purpose of the Study:

  • To investigate the genomic distribution and regulation of dormant origins.
  • To identify molecular determinants of origin efficiency under replicative stress.

Main Methods:

  • Analysis of origin activity in mouse embryonic stem cells under normal and stress conditions (aphidicolin, CDC6 deregulation).
  • Comparison of genetic and epigenetic features of origins with varying activation levels.
  • Integration of genomic positions with 3D chromatin interaction data (Hi-C, promoter-capture Hi-C).

Main Results:

  • Stress-responsive origins are often active at low frequency in normal S phase.
  • Replicative stress increases the activation frequency of these origins.
  • Origin efficiency is proportional to proximity to transcriptional start sites and chromatin interaction frequency.

Conclusions:

  • Dormant origins are pre-activated in a subset of cells during normal S phase.
  • Origin efficiency is influenced by genomic location and 3D chromatin organization.
  • Findings support the model of DNA replication origins organized in higher-order replication factories.