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

You might also read

Related Articles

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

Sort by
Same author

Smart double-screening system of propagating male-sterile lines for maize hybrid seed production.

Journal of integrative plant biology·2026
Same author

Regulation of spikelet number during wheat spike development.

bioRxiv : the preprint server for biology·2026
Same author

MicroRNA156 and its targeted SPL genes interact with the photoperiod, vernalization, and gibberellin pathways to regulate wheat heading time.

The Plant journal : for cell and molecular biology·2026
Same author

Dosa: A method to covalently barcode proteins for high-throughput biochemistry.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Genome-assisted identification of wheat leaf rust resistance gene Lr.ace-4A/Lr30.

Nature communications·2025
Same author

Dosa: A method to covalently barcode proteins for high throughput biochemistry.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jul 29, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
12:33

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

12.9K

Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.

Juan M Debernardi1,2, German Burguener3,4, Kerry Bubb5

  • 1University of California, Davis, CA, 95616, USA. jmdebernardi@ucdavis.edu.

BMC Plant Biology
|May 21, 2023
PubMed
Summary

We developed a new method combining INTACT and ATAC-seq for identifying regulatory elements in wheat. This approach maps open chromatin regions, aiding in understanding gene regulation and improving genome functionality insights.

Keywords:
ATAC-seqINTACTOpen chromatinRegulatory regionsWheat

More Related Videos

Development of Targeting Induced Local Lesions IN Genomes TILLING Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis
08:36

Development of Targeting Induced Local Lesions IN Genomes TILLING Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis

Published on: July 16, 2019

11.7K
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
06:22

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

Published on: August 25, 2020

12.4K

Related Experiment Videos

Last Updated: Jul 29, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
12:33

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

12.9K
Development of Targeting Induced Local Lesions IN Genomes TILLING Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis
08:36

Development of Targeting Induced Local Lesions IN Genomes TILLING Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis

Published on: July 16, 2019

11.7K
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
06:22

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

Published on: August 25, 2020

12.4K

Area of Science:

  • Plant genomics
  • Epigenetics
  • Molecular biology

Background:

  • Genetic information in organisms is organized by genes and regulatory elements.
  • Cis-regulatory elements are crucial for gene expression but remain poorly characterized in plants.
  • Chromatin accessibility is a key indicator for identifying these regulatory elements.

Purpose of the Study:

  • To develop a method for identifying cis-regulatory elements in tetraploid wheat.
  • To characterize open chromatin regions in wheat using a novel technique.
  • To improve the understanding of wheat genome functionality.

Main Methods:

  • Developed a transgenic INTACT (isolation of nuclei tagged in specific cell types) system for nuclei purification in tetraploid wheat.
  • Combined the INTACT system with ATAC-seq (assay for transposase-accessible chromatin with sequencing) to map open chromatin.
  • Analyzed ATAC-seq data from wheat root tips.

Main Results:

  • Successfully purified nuclei from wheat root tips using the INTACT system.
  • Identified open chromatin regions, predominantly in intergenic and promoter areas, consistent with regulatory elements.
  • Demonstrated high reproducibility and overlap of open chromatin regions between root and leaf tissues.
  • Observed overlap between ATAC-seq peaks and validated cis-regulatory elements, correlating accessibility with gene expression.

Conclusions:

  • Established and validated an INTACT system for efficient nuclei isolation in tetraploid wheat.
  • ATAC-seq experiments using INTACT-purified nuclei revealed open chromatin regions, aiding cis-regulatory element identification.
  • The INTACT system facilitates broader ATAC-seq dataset generation for a comprehensive map of accessible DNA in the wheat genome.