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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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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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Lagging Strand Synthesis01:59

Lagging Strand Synthesis

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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
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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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Replication in Prokaryotes01:32

Replication in Prokaryotes

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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...
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DNA Replication02:40

DNA Replication

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DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied.  After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
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DNA replication...
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Related Experiment Video

Updated: Sep 6, 2025

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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Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.

Juan Carlos Rivera-Mulia1,2,3, Claudia Trevilla-Garcia4, Santiago Martinez-Cifuentes4

  • 1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA. riveramj@umn.edu.

Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology
|July 5, 2022
PubMed
Summary
This summary is machine-generated.

Researchers developed a new, cost-effective method to measure genome-wide replication timing (RT) in low-input samples. This high-resolution technique improves RT analysis for gene function, nuclear architecture, and disease studies.

Keywords:
DNA replicationgenomicslibrary preparationnext-generation sequencingreplication timing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Replication timing (RT) is a cell type-specific program of genome duplication during S-phase.
  • RT is linked to genome organization, gene activity, development, and disease.
  • Existing RT methods require large cell numbers or are low-throughput and costly.

Purpose of the Study:

  • To develop an improved, high-resolution method for genome-wide replication timing analysis.
  • To enable RT studies in samples with limited cell numbers.
  • To provide standardized parameters for RT measurement.

Main Methods:

  • Developed a streamlined protocol integrating cell sorting, DNA fragmentation, and library preparation in a single tube.
  • Optimized a systematic data processing pipeline for standardized RT measurement.
  • Applied the method to enable high-resolution, low-input genome-wide RT analysis.

Main Results:

  • The new method significantly increases yield, quality, and reproducibility.
  • It reduces costs and complexity compared to existing single-cell RT analyses.
  • Achieved high-resolution genome-wide RT measurement from low cell input.

Conclusions:

  • This optimized method overcomes limitations of previous RT assays.
  • It facilitates broader application of RT analysis in diverse biological contexts.
  • Enables new insights into RT's role in gene regulation, nuclear organization, and disease.