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The DNA Replication Fork01:02

The DNA Replication Fork

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 forks, one in...
The DNA Replication Fork01:02

The DNA Replication Fork

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 forks, one in...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

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, a...
Chromosome Replication02:31

Chromosome Replication

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 of...
Replication in Eukaryotes01:29

Replication in Eukaryotes

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.
Many Proteins Orchestrate Replication at the Origin
Eukaryotic replication follows many of the same...
Replication in Eukaryotes02:31

Replication in Eukaryotes

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Related Experiment Video

Updated: May 24, 2026

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization
17:14

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

Published on: December 10, 2012

USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator.

Vahideh Hassan-Zadeh1, Sabarinadh Chilaka, Jean-Charles Cadoret

  • 1Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France.

Plos Biology
|March 14, 2012
PubMed
Summary

Insulator elements, like the HS4 insulator, can advance DNA replication timing in late-replicating regions. This effect depends on the insulator

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Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
08:06

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

Published on: January 19, 2017

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Related Experiment Videos

Last Updated: May 24, 2026

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization
17:14

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

Published on: December 10, 2012

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
08:06

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

Published on: January 19, 2017

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Vertebrate DNA replication timing is organized by isochore composition, with GC-rich regions replicating early and AT-rich regions late.
  • Gene density and active transcription correlate with early replication, suggesting a link between gene regulation and replication timing.
  • Insulator elements, known to organize transcriptional domains, are hypothesized to regulate replication timing.

Purpose of the Study:

  • To investigate the role of the β-globin HS4 insulator in modulating replication timing of late-replicating genomic regions.
  • To determine if insulator elements can impose an earlier replication timing on endogenous loci.
  • To identify the specific cis-elements within the HS4 insulator responsible for replication timing control.

Main Methods:

  • Insertion of a replication origin flanked by the β-globin HS4 insulator into late-replicating regions in avian cell lines (DT40 and 6C2).
  • Analysis of replication timing shifts using established molecular biology techniques.
  • Mutation analysis to pinpoint key cis-elements within the HS4 insulator, focusing on transcription factor binding sites.

Main Results:

  • The HS4 insulator significantly advances the replication timing of target loci from late S-phase to early S-phase.
  • This replication timing shift requires the presence of HS4 on both sides of the replication origin.
  • The USF transcription factor binding site within HS4 was identified as the critical element controlling replication timing.
  • The presence of a nearby transcribed gene enhances the effect of the insulator on replication timing.

Conclusions:

  • The β-globin HS4 insulator can reprogram replication timing, shifting late-replicating regions to an earlier S-phase.
  • Specific cis-elements within insulators, particularly USF binding sites, are key regulators of replication timing.
  • These findings suggest a model where insulators contribute to the formation of early replication domains.