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

CRISPR01:59

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced Short...
Homologous Recombination02:31

Homologous Recombination

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...
CRISPR and crRNAs02:53

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
CRISPR01:59

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced Short...
CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...

You might also read

Related Articles

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

Sort by
Same author

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing.

medRxiv : the preprint server for health sciences·2026
Same author

Biological aging and generational shifts in early-onset cancer risk.

Nature medicine·2026
Same author

RAG-mediated structural variation and its impact on relapse risk in acute lymphoblastic leukemia.

medRxiv : the preprint server for health sciences·2026
Same author

Shifting IRES versus Cap-initiated translation during homeostatic stem cell differentiation and stress.

Science advances·2026
Same author

Transcription factor collaboration enables precise T cell state engineering.

bioRxiv : the preprint server for biology·2026
Same author

Proximity-Induced Rewiring of Oncogenic Kinase Triggers Apoptosis.

ACS central science·2026

Related Experiment Video

Updated: Jun 6, 2026

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

11.6K

Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.

Heejin Roh1,2, Simon P Shen1,2, Yan Hu2,3

  • 1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Nature Methods
|September 11, 2025
PubMed
Summary

We developed targeted deaminase-accessible chromatin sequencing (TDAC-seq) to profile chromatin accessibility in single DNA molecules. This genome editing method links genetic changes to chromatin accessibility with single-nucleotide resolution.

More Related Videos

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

4.1K
ATAC-Seq Optimization for Cancer Epigenetics Research
07:13

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

5.2K

Related Experiment Videos

Last Updated: Jun 6, 2026

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

11.6K
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

4.1K
ATAC-Seq Optimization for Cancer Epigenetics Research
07:13

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

5.2K

Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Genome editing advances understanding of cis-regulatory elements.
  • Current methods struggle to profile chromatin accessibility on single, long DNA molecules.

Purpose of the Study:

  • To develop a method for profiling chromatin accessibility at specific genomic loci on single chromatin fibers.
  • To link genome editing outcomes to chromatin accessibility changes at single-nucleotide resolution.

Main Methods:

  • Developed targeted deaminase-accessible chromatin sequencing (TDAC-seq) using cytidine deaminases.
  • Applied TDAC-seq with CRISPR perturbations for sequence-function mapping.
  • Utilized long-read sequencing for high-resolution analysis of targeted loci.

Main Results:

  • TDAC-seq successfully profiled chromatin accessibility at endogenous loci.
  • Integrated TDAC-seq with CRISPR edits to map effects on fetal hemoglobin activation in HSPCs.
  • Applied TDAC-seq to analyze variants in a GFI1B enhancer linked to myeloproliferative neoplasms.

Conclusions:

  • TDAC-seq provides high-resolution, single-molecule mapping of chromatin accessibility.
  • The method enables linking genome editing to chromatin accessibility changes.
  • TDAC-seq is a scalable tool for interrogating regulatory element function and disease-associated variants.