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

RNA Editing02:23

RNA Editing

9.2K
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...
9.2K
Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

7.2K
Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
7.2K
Mismatch Repair01:20

Mismatch Repair

5.3K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
5.3K
Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

241
Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
241
Animal Mitochondrial Genetics02:59

Animal Mitochondrial Genetics

8.1K
Among all the organelles in an animal cell, only mitochondria have their own independent genomes. Animal mitochondrial DNA is a double-stranded, closed-circular molecule with around 20,000 base pairs. Mitochondrial DNA is unique in that one of its two strands, the heavy, or H, -strand is guanine rich, whereas the complementary strand is cytosine rich and called the light, or L, -strand. Compared to nuclear DNA, mitochondrial DNA has a very low percentage of non-coding regions and is marked by...
8.1K
Base Excision Repair01:54

Base Excision Repair

23.1K
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...
23.1K

You might also read

Related Articles

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

Sort by
Same author

Author Correction: Long-term, in toto live imaging of cardiomyocyte behaviour during mouse ventricle chamber formation at single-cell resolution.

Nature cell biology·2026
Same author

Cell-free chromatin state tracing reveals disease origin and therapy responses.

Nature·2026
Same author

Quantitative analysis of small RNA pseudouridylation reveals interplay of PUS enzymes in tRNA anticodon stem-loop.

Nature communications·2026
Same author

Single-strand deaminase-assisted editing for functional RNA manipulation.

Nature biotechnology·2026
Same author

CRISPR-free RNA base editing mediated PTC-readthrough restores hearing in mice with Otof nonsense mutation.

Nature communications·2025
Same author

Pt-seq unveils the genomic binding pattern of platinum-based drugs.

Science advances·2025

Related Experiment Video

Updated: Sep 23, 2025

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors
09:22

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

5.6K

Mitochondrial base editor induces substantial nuclear off-target mutations.

Zhixin Lei1,2, Haowei Meng3, Lulu Liu3

  • 1Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.

Nature
|May 13, 2022
PubMed
Summary
This summary is machine-generated.

DddA-derived cytosine base editors (DdCBEs) can edit mitochondrial DNA but cause widespread unintended edits in the nuclear genome. Researchers identified hundreds of off-target sites, some dependent on TALE array sequences and others linked to CTCF binding sites.

More Related Videos

An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model
06:05

An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model

Published on: March 9, 2022

3.9K
Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

1.6K

Related Experiment Videos

Last Updated: Sep 23, 2025

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors
09:22

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

5.6K
An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model
06:05

An In Vitro Approach to Study Mitochondrial Dysfunction: A Cybrid Model

Published on: March 9, 2022

3.9K
Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

1.6K

Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • DddA-derived cytosine base editors (DdCBEs) are engineered proteins for targeted C•G-to-T•A conversions in mitochondrial DNA.
  • The genome-wide specificity and potential off-target effects of DdCBEs remain largely uncharacterized.

Purpose of the Study:

  • To comprehensively analyze the genome-wide specificity of DdCBEs.
  • To identify and characterize off-target editing events in both nuclear and mitochondrial DNA.
  • To investigate the mechanisms underlying off-target editing and explore strategies for mitigation.

Main Methods:

  • Genome-wide, unbiased analysis of the DdCBE editome.
  • Identification of TALE array sequence (TAS)-dependent and TAS-independent off-target sites.
  • Analysis of off-target site localization relative to genomic features like CTCF binding sites and topologically associating domain boundaries.

Main Results:

  • DdCBEs induce extensive off-target editing in the nuclear genome, with hundreds of identified sites.
  • Off-target sites can be TAS-dependent, with some specified by single TALE repeats, challenging existing models.
  • TAS-independent off-target sites are frequently shared across different DdCBEs and co-localize with CTCF binding sites and TAD boundaries.

Conclusions:

  • The widespread nuclear off-target activity of DdCBEs necessitates careful evaluation for research and therapeutic applications.
  • Understanding the mechanisms of off-target editing, including TAS-dependent and independent pathways, is crucial.
  • Engineering DdCBEs to reduce off-target effects is essential for their safe and effective use in genome editing.