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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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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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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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Updated: Mar 8, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Capitalizing on disaster: Establishing chromatin specificity behind the replication fork.

Srinivas Ramachandran1,2, Kami Ahmad1, Steven Henikoff1,2

  • 1Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology
|January 31, 2017
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Summary

Genomic activity relies on precise chromatin organization. DNA replication transiently disrupts chromatin, creating a window for specific transcription factor binding during its reassembly.

Keywords:
chromatinepigenetics

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Eukaryotic genomes are organized into nucleosomal chromatin, essential for genomic activity.
  • DNA replication in the S phase transiently disrupts localized chromatin features.
  • Histone deposition and chromatin reassembly occur rapidly behind replication forks.

Purpose of the Study:

  • To investigate the impact of DNA replication on locus-specific chromatin features.
  • To understand the timing and specificity of transcription factor binding post-replication.
  • To propose a model for how chromatin reassembly influences regulatory element accessibility.

Main Methods:

  • Genomic strategies were employed to observe chromatin rebuilding.
  • Analysis of transcription factor binding dynamics behind replication forks.

Main Results:

  • Localized chromatin features are transiently obliterated by DNA replication.
  • Surprising delays in transcription factor binding were observed behind replication forks.
  • Transient chromatin disorganization during replication appears critical for targeted transcription factor binding.

Conclusions:

  • The transient disorganization of chromatin during replication is a key juncture for specific transcription factor binding.
  • The proposed model suggests that disorganized nucleosomes transiently occlude regulatory elements, enforcing binding specificity during chromatin maturation.