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Related Concept Videos

The DNA Replication Fork01:02

The DNA Replication Fork

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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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Replication in Eukaryotes01:29

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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
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Related Experiment Video

Updated: Mar 24, 2026

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System
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RF-SIRF reveals a replication stress-specific epigenetic code by spatio-temporal mapping of reversed forks.

Sunetra Roy1, Morgan M Fimreite1, Yue Chen1

  • 1Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA.

Nature Communications
|March 23, 2026
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Scientists developed a new method, Reversed Fork Site-specific Identification and Retrieval (RF-SIRF), to map reversed forks (RFs) in cells. This technique reveals how RFs are crucial for genomic stability and DNA repair during replication stress.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • DNA replication stress responses are vital for genomic stability, impacting development, aging, and disease.
  • Reversed forks (RFs) are key structures formed during replication stalling, protecting DNA from damage.
  • Existing methods for RF detection, like electron microscopy, limit in-situ cellular studies.

Purpose of the Study:

  • To develop a novel, quantitative method for mapping RFs with single-cell resolution.
  • To investigate the cellular localization, chromatin environment, and epigenetic regulation of RFs.
  • To enable detailed proteomic and spatial analyses of RFs in their native context.

Main Methods:

  • Development and application of a new technique called RF-SIRF (Reversed Fork Site-specific Identification and Retrieval).
  • Utilizing the biophysical properties of RFs for detection and mapping.
  • Single-cell resolution analysis of RFs within the cellular environment.

Main Results:

  • RF-SIRF successfully mapped RFs with single-cell resolution.
  • RFs were observed to accumulate at the nuclear periphery during early to mid-S phase.
  • RFs exhibit a unique chromatin landscape and an epigenetic code distinct from transcription.

Conclusions:

  • RF-SIRF provides a robust tool for quantitative, temporal, and spatial analysis of RFs.
  • The findings highlight a specialized epigenetic code at RFs that recruits DNA stress response proteins.
  • This method advances the study of DNA replication stress responses and their role in cellular and medical contexts.