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

DNA Isolation01:24

DNA Isolation

43.2K
DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
43.2K
DNA Isolation01:34

DNA Isolation

196.1K
DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.
196.1K

You might also read

Related Articles

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

Sort by
Same author

FOXM1 inhibition primes terminal differentiation of human iPSC-derived hepatocytes.

Cell death discovery·2026
Same author

Optimization of a hybridization-based target enrichment protocol for precision oncology.

Molecular biology reports·2026
Same author

Role of CNTN6 in neurodevelopment and neuropathology.

Frontiers in neuroscience·2026
Same author

Chromosome-level genome assembly of the sand martin (Riparia riparia).

Scientific data·2026
Same author

The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.

Nucleic acids research·2026
Same author

Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation.

Molecular omics·2026

Related Experiment Video

Updated: Nov 12, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

410.4K

A cookbook for DNase Hi-C.

Maria Gridina1, Evgeniy Mozheiko1, Emil Valeev1,2

  • 1Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia.

Epigenetics & Chromatin
|March 21, 2021
PubMed
Summary

This study introduces an improved DNAse Hi-C protocol for studying 3D chromatin architecture. The optimized method enhances efficiency and reduces costs for genome assembly and analysis.

Keywords:
A549DNAse IGenome organizationHi-CHuman peripheral bloodK562LNCaP

More Related Videos

In-Nucleus Hi-C in Drosophila Cells
11:58

In-Nucleus Hi-C in Drosophila Cells

Published on: September 15, 2021

4.4K
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
10:16

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

33.0K

Related Experiment Videos

Last Updated: Nov 12, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

410.4K
In-Nucleus Hi-C in Drosophila Cells
11:58

In-Nucleus Hi-C in Drosophila Cells

Published on: September 15, 2021

4.4K
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
10:16

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

33.0K

Area of Science:

  • Genomics and Molecular Biology
  • Epigenetics and Chromatin Structure

Background:

  • The Hi-C technique is crucial for understanding 3D chromatin organization and genome assembly.
  • Conventional Hi-C uses restriction enzymes, leading to uneven genomic coverage.
  • Sequence-agnostic enzymes like DNAse I offer a potential solution to improve coverage uniformity.

Purpose of the Study:

  • To compare and optimize different DNAse Hi-C protocols.
  • To identify critical steps influencing protocol efficiency and library quality.
  • To develop a robust and cost-effective DNAse Hi-C library preparation method.

Main Methods:

  • Comparative analysis of various DNAse Hi-C protocols.
  • Investigation of critical steps, including SDS quenching and adapter design.
  • Implementation of nucleotide-exchange enzymes for DNA end repair and labeling.

Main Results:

  • SDS quenching strategy significantly impacts chromatin digestion efficiency.
  • Optimized adapter design minimizes ligase reaction by-products.
  • Nucleotide-exchange enzymes streamline DNA end processing, simplifying the protocol.

Conclusions:

  • A new, robust DNAse Hi-C protocol is proposed for human cell and blood samples.
  • The protocol incorporates experimental controls and computational tools for quality evaluation.
  • Improvements lead to a less expensive and more time-efficient library preparation process.