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Related Experiment Video

Updated: Aug 9, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.

Georgi K Marinov1, Zohar Shipony2, Anshul Kundaje2,3

  • 1Department of Genetics, Stanford University, Stanford, CA, USA. marinovg@stanford.edu.

Methods in Molecular Biology (Clifton, N.J.)
|February 22, 2023
PubMed
Summary

This study details optimal practices for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) experiments. It focuses on identifying active cis-regulatory elements by mapping accessible chromatin regions in mammalian systems.

Keywords:
ATAC-seqChromatin accessibilityEnhancersHigh-throughput sequencingPromoters

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Active cis-regulatory elements (cREs) are crucial for gene regulation in eukaryotes.
  • These elements exhibit nucleosomal depletion, leading to higher DNA accessibility.
  • Accessible chromatin mapping is vital for understanding cellular states and gene regulation.

Purpose of the Study:

  • To provide optimal practices and considerations for conducting ATAC-seq experiments.
  • To highlight the utility of ATAC-seq for identifying active cREs genome-wide.
  • To standardize ATAC-seq methodologies, particularly in mammalian systems.

Main Methods:

  • Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is the primary method discussed.
  • The method leverages preferential enzymatic cleavage/labeling of accessible DNA.
  • Focus on genome-wide mapping of open chromatin regions.

Main Results:

  • ATAC-seq has become the standard tool for mapping open chromatin.
  • Nucleosomal depletion is a key characteristic of active cREs.
  • The method allows tracking of cRE dynamics across cellular states.

Conclusions:

  • Optimal ATAC-seq practices are essential for reliable identification of active cREs.
  • ATAC-seq is a versatile and adaptable method for chromatin accessibility studies.
  • Adherence to best practices ensures accurate mapping of regulatory elements in mammalian genomes.