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Related Concept Videos

DNA Isolation01:24

DNA Isolation

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...

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Related Experiment Video

Updated: Jun 17, 2026

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
08:08

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

Published on: April 2, 2018

Formaldehyde-assisted isolation of regulatory elements.

Peter L Nagy1, David H Price1

  • 1Departments of Pathology, Biochemistry and Pediatrics, University of Iowa, Iowa City, IA 52242, USA.

Wiley Interdisciplinary Reviews. Systems Biology and Medicine
|January 5, 2010
PubMed
Summary
This summary is machine-generated.

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) identifies accessible DNA in chromatin. This method reveals cell-specific regulatory regions and novel chromatin structures, aiding in understanding gene regulation and disease.

Keywords:
DNase I sensitivityFAIREchromatin structureformaldehyde crosslinkinggenome organizationnucleosome distributionregulatory sequencestranscription

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Related Experiment Videos

Last Updated: Jun 17, 2026

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
08:08

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Published on: April 2, 2018

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP
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Published on: January 20, 2016

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Chromatin structure influences DNA accessibility and gene regulation.
  • Histones, abundant chromatin proteins, readily crosslink with DNA upon formaldehyde treatment.
  • Locus-specific variations in DNA trapping reflect chromatin's protein composition and accessibility.

Purpose of the Study:

  • To describe and validate the Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) method.
  • To identify physically accessible DNA segments in the eukaryotic genome.
  • To explore the cell type-specific nature of chromatin accessibility patterns.

Main Methods:

  • Utilizes formaldehyde treatment to crosslink proteins to DNA.
  • Isolates DNA fragments based on differential protein trapping, reflecting chromatin accessibility.
  • Analyzes enriched DNA fragments using techniques like massively parallel sequencing.

Main Results:

  • FAIRE successfully identifies and enriches for physically accessible DNA segments.
  • Detected fragments largely correspond to DNaseI hypersensitive sites in active chromatin.
  • FAIRE also identifies accessible regions in repressed chromatin and novel structural sites.

Conclusions:

  • FAIRE is a simple yet powerful method for probing chromatin structure and DNA accessibility.
  • FAIRE-identified regions are cell type-specific, offering insights into tissue-specific gene regulation.
  • The method holds potential for discovering regulatory elements and understanding chromatin's role in disease.