Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

The Replisome03:01

The Replisome

9.9K
9.9K
The Replisome03:01

The Replisome

31.2K
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...
31.2K
DNA Replication02:40

DNA Replication

54.3K
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.
Replication in Prokaryotes
DNA replication...
54.3K
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

5.1K
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,...
5.1K
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

1.4K
1.4K
Next-generation Sequencing03:00

Next-generation Sequencing

87.9K
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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Topological stress regulates replication fork dynamics in unperturbed S phase.

Nature communications·2026
Same author

Transcription elongation can be sufficient, but is not necessary, to advance replication timing.

EMBO reports·2026
Same author

Parallel analysis of replication timing, gene expression, and copy number with PARTAGE.

Genome research·2026
Same author

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method.

Journal of visualized experiments : JoVE·2026
Same author

Proximal proteomics analysis reveals DNA polymerase δ subunit 3 is a new MCM2 binding partner and promotes parental histones inheritance in mammalian cells.

Cell death and differentiation·2025
Same author

The long-standing relationship between replication timing, gene expression, and chromatin accessibility is maintained in early mouse embryogenesis.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: May 5, 2026

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

7.8K

REPLAY: A reproducible and user-friendly application for DNA replication timing analysis from Repli-seq data.

Quinn Dickinson1,2, Chuanhe Yu2, Juan Carlos Rivera-Mulia1,3,4,5

  • 1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota.

Biorxiv : the Preprint Server for Biology
|May 4, 2026
PubMed
Summary

REPLAY is a new, automated application for analyzing DNA replication timing (RT) data. It simplifies complex Repli-seq analysis into a user-friendly workflow, improving reproducibility and accessibility for researchers.

Keywords:
ApptainerDNA replication timingRepli-seqautomated workflowepigenomegenomicsreproducibility

More Related Videos

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

5.0K
Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System
10:17

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Published on: April 30, 2018

7.0K

Related Experiment Videos

Last Updated: May 5, 2026

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

7.8K
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

5.0K
Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System
10:17

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Published on: April 30, 2018

7.0K

Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • DNA replication timing (RT) is crucial for genome organization and is often dysregulated in diseases.
  • Current Repli-seq analysis methods are complex, requiring multiple tools and scripting, hindering reproducibility and accessibility.
  • Existing workflows lack standardization and demand significant user intervention, posing challenges for non-expert users.

Purpose of the Study:

  • To develop an automated, reproducible, and user-friendly application for genome-wide replication timing analysis.
  • To streamline the end-to-end processing of Repli-seq data, from raw reads to RT profiles.
  • To lower the barrier to entry for RT data analysis, enabling broader adoption and standardization.

Main Methods:

  • Developed REPLAY, a standalone executable application for automated RT analysis.
  • Integrated all essential processing steps: quality control, trimming, alignment, binning, RT log2 calculation, normalization, smoothing, and visualization.
  • Provided an intuitive graphical interface for easy parameter configuration without requiring programming experience.

Main Results:

  • REPLAY enables end-to-end processing of FASTQ files to genome-wide RT profiles.
  • The application demonstrated accurate reconstruction of RT profiles and high reproducibility across diverse datasets.
  • REPLAY successfully integrated all analysis steps into a single, automated workflow.

Conclusions:

  • REPLAY provides a portable, reproducible, and accessible solution for replication timing data analysis.
  • By eliminating the need for command-line tools and complex installations, REPLAY democratizes RT analysis.
  • The application promotes standardized analysis across various research settings, enhancing scientific collaboration and discovery.