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Related Concept Videos

The Replisome03:01

The Replisome

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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
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The Replisome03:01

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Restarting Stalled Replication Forks02:37

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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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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Chromosome Replication02:31

Chromosome 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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Homologous Recombination02:31

Homologous Recombination

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Related Experiment Video

Updated: Feb 25, 2026

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

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Repliscan: a tool for classifying replication timing regions.

Gregory J Zynda1, Jawon Song1, Lorenzo Concia2

  • 1Texas Advanced Computing Center, University of Texas at Austin, 10100 Burnet Road, Austin, 78758-4497, TX, USA.

BMC Bioinformatics
|August 9, 2017
PubMed
Summary
This summary is machine-generated.

We developed Repliscan, a robust tool for analyzing replication timing data. It accurately detects and classifies genomic replication regions, outperforming traditional methods for improved biological insights.

Keywords:
ClassificationDNA replicationRepli-seq

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

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Replication timing experiments generate data similar to ChIP-Seq.
  • Traditional ChIP-Seq analysis is unsuitable for replication timing data due to experimental differences.

Purpose of the Study:

  • To develop a robust method for analyzing replication timing data.
  • To accurately detect and classify replication regions across the genome.

Main Methods:

  • Repliscan normalizes data and removes outliers.
  • It classifies Repli-seq signals into replication signatures.
  • Quality control and self-fitting methods enhance applicability.

Main Results:

  • Repliscan accurately detects and classifies genomic replication regions.
  • It is more robust than threshold-based methods.
  • The tool provides reliable replication profiles.

Conclusions:

  • Repliscan is effective across different genome sizes.
  • Reliable profiles are generated with minimal coverage (2.4x) and small window sizes (1kb).
  • The method is simple and broadly applicable.