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Updated: May 16, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing.

Georgi K Marinov¹, William J Greenleaf^1,2,3,4,5

¹Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.

|May 14, 2025

Summary

This summary is machine-generated.

The KAS-ATAC assay maps DNA fragments that are both physically accessible and contain single-stranded DNA (ssDNA) bubbles. This method aids in understanding gene regulation by identifying active cis-regulatory elements and RNA polymerase activity.

Keywords:

ATAC-seq Chromatin Chromatin accessibility KAS-ATAC KAS-seq Transcription ssDNA

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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

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Published on: November 13, 2017

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Gene regulation involves cis-regulatory elements (cREs) and RNA polymerase activity.
Active cREs are often nucleosome-depleted and bound by transcription factors.
RNA polymerase activity can create single-stranded DNA (ssDNA) structures.

Purpose of the Study:

To present a detailed protocol for the KAS-ATAC assay.
To describe the basic processing of KAS-ATAC datasets.
To discuss key considerations for successful KAS-ATAC application.

Main Methods:

KAS-ATAC assay captures DNA fragments with both physical accessibility and ssDNA bubbles.
Involves N3-kethoxal labeling and transposition of native chromatin.
Includes biotin-labeled DNA fragment pulldown and library generation.

Main Results:

The protocol enables mapping of simultaneously accessible and ssDNA-containing DNA fragments.
Detailed steps for N3-kethoxal labeling and chromatin transposition are provided.
Methods for DNA fragment pulldown and library preparation are described.

Conclusions:

KAS-ATAC is a valuable method for studying gene regulatory processes.
The protocol facilitates the investigation of active cREs and RNA polymerase association with DNA.
Successful application requires careful consideration of protocol execution and data processing.