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 DNA Replication Fork01:02

The DNA Replication Fork

36.3K
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...
36.3K
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

5.9K
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,...
5.9K
Replication in Prokaryotes01:32

Replication in Prokaryotes

25.1K
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...
25.1K
Replication in Eukaryotes01:29

Replication in Eukaryotes

14.1K
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...
14.1K
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

53.7K
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...
53.7K
The Replisome03:01

The Replisome

34.2K
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...
34.2K

You might also read

Related Articles

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

Sort by
Same author

ATR and TopBP1 oppose to control dormant origin activity and global replication dynamics, providing a first defense against replication stress.

Nucleic acids research·2026
Same author

High-resolution HIV-1 m<sup>6</sup>A epitranscriptome reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications.

NAR genomics and bioinformatics·2025
Same author

Regulated TRESLIN-MTBP loading governs initiation zones and replication timing in human DNA replication.

Nature communications·2025
Same author

m6A modification in R-loop homeostasis: a potential target for cancer therapeutics.

NAR cancer·2025
Same author

Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.

Nature communications·2025
Same author

Maternal inheritance of functional centrioles in two parthenogenetic nematodes.

Nature communications·2024
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Aug 14, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

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

Published on: May 2, 2025

460

OKseqHMM: a genome-wide replication fork directionality analysis toolkit.

Yaqun Liu1, Xia Wu1, Yves d'Aubenton-Carafa2

  • 1Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France.

Nucleic Acids Research
|January 11, 2023
PubMed
Summary
This summary is machine-generated.

A new bioinformatics toolkit, OKseqHMM, analyzes Okazaki fragment sequencing data to map genome-wide replication fork directionality. This tool helps identify transcription-replication conflicts, crucial for understanding genome instability and human health.

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

5.9K
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

8.5K

Related Experiment Videos

Last Updated: Aug 14, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

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

Published on: May 2, 2025

460
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

5.9K
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

8.5K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • DNA replication is essential for cell division, involving coordinated origin activation.
  • Replication fork progression faces challenges from transcription-replication conflicts (TRCs), especially head-on TRCs, which threaten genome integrity.

Purpose of the Study:

  • To develop a bioinformatics toolkit for analyzing replication fork directionality and transcription-replication conflicts.
  • To enable accurate prediction of replication initiation and termination genome-wide.

Main Methods:

  • Development of the OKseqHMM bioinformatics toolkit.
  • Analysis of Okazaki fragment sequencing datasets to measure genome-wide replication fork directionality (RFD).
  • Application of OKseqHMM to other RFD-containing genome-wide sequencing techniques (e.g., eSPAN, TrAEL-seq).

Main Results:

  • OKseqHMM accurately measures genome-wide RFD, replication initiation, and termination.
  • The toolkit successfully analyzed diverse datasets across yeast, mouse, and human cells.
  • Identified loci at risk of TRCs, particularly head-on TRCs, by comparing replication and transcription directions.

Conclusions:

  • OKseqHMM is a versatile tool for studying replication dynamics and TRCs across various cell models and conditions.
  • The toolkit facilitates the investigation of TRCs' role in genome instability and DNA damage.
  • Findings are significant for understanding human health and disease related to genomic integrity.