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

Mismatch Repair01:36

Mismatch Repair

40.1K
Overview
40.1K
Proofreading01:43

Proofreading

54.1K
Overview
54.1K
Base Excision Repair01:54

Base Excision Repair

22.4K
One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
22.4K
Next-generation Sequencing03:00

Next-generation Sequencing

89.0K
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....
89.0K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

10.6K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
10.6K
RNA Editing02:23

RNA Editing

9.0K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
9.0K

You might also read

Related Articles

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

Sort by
Same author

Nephrologist follow-up improves outcomes after hospitalization with acute kidney injury.

BMC nephrology·2026
Same author

Emergence of azithromycin-resistant extensively drug-resistant <i>Salmonella</i> Kentucky ST314 in Taiwan.

Frontiers in microbiology·2026
Same author

Plasmid-borne transcriptional regulator RamAp modulates <i>Salmonella</i> genes for environmental and host adaptation.

Frontiers in microbiology·2026
Same author

Perioperative management of biologic disease-modifying antirheumatic drugs in patients with inflammatory rheumatic diseases undergoing total joint arthroplasty: A nationwide population-based cohort study from Taiwan.

Seminars in arthritis and rheumatism·2026
Same author

Adequate canal-filling ratio and extension stem length reduce radiographic loosening in revision total knee arthroplasty using hybrid fixation with grit-blasted, fluted stems.

The Knee·2026
Same author

Sodium Bicarbonate for Acute Metabolic Acidosis in Critically Ill Adults: A Meta-Analysis of Randomized Clinical Trials.

Critical care medicine·2026

Related Experiment Video

Updated: Jul 9, 2025

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

8.8K

Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based

Chien-Shun Chiou1, Bo-Han Chen1, You-Wun Wang1

  • 1Centers for Disease Control, Taichung, Taiwan.

Communications Biology
|November 29, 2023
PubMed
Summary
This summary is machine-generated.

Novel DNA modifications can reduce Oxford Nanopore Technology (ONT) sequencing quality. A new method, Modpolish, corrects these errors while preserving epigenome data, improving both in-house and public datasets.

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.1K
Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study
06:57

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Published on: July 7, 2023

1.1K

Related Experiment Videos

Last Updated: Jul 9, 2025

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

8.8K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.1K
Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study
06:57

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Published on: July 7, 2023

1.1K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Oxford Nanopore Technology (ONT) sequencing accuracy has improved with advancements in flowcells, kits, and basecalling.
  • However, novel DNA modifications not recognized by basecalling models can significantly degrade sequence quality.

Purpose of the Study:

  • To investigate the impact of novel modification types on ONT sequencing quality.
  • To develop and evaluate methods for correcting modification-induced errors while preserving epigenome information.

Main Methods:

  • Whole-genome amplification for demodification.
  • Development of Modpolish, a reference-based method for modification error correction.
  • Evaluation of Modpolish on in-house and public ONT datasets (R9.4 and R10.4 simplex).

Main Results:

  • Novel modification types were identified as a cause of unexpected low quality in ONT-sequenced genomes.
  • Demodification via whole-genome amplification improved quality but resulted in epigenome loss.
  • Modpolish effectively corrected modification-mediated errors, retaining epigenome data, and improved quality across various datasets.

Conclusions:

  • Novel DNA modifications are a significant source of systematic errors in ONT sequencing.
  • These errors are correctable using nucleotide demodification or the Modpolish method, even without prior knowledge of the modifications.
  • Modpolish offers a valuable solution for improving ONT data quality while preserving crucial epigenomic information.