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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq
Georgi K Marinov1, Zohar Shipony2
1Department of Genetics, Stanford University, Stanford, CA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|February 19, 2021
Summary
Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a key method for mapping chromatin accessibility and cis-regulatory element activity. This review details standard computational analysis procedures and best practices for ATAC-seq data.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a powerful technique for genome-wide profiling of open chromatin regions.
- It is widely used to study cis-regulatory element (cRE) activity across diverse biological systems.
- The increasing application of ATAC-seq has led to the accumulation of significant data and the emergence of standard analytical workflows.
Purpose of the Study:
- To review common computational procedures for ATAC-seq data analysis.
- To provide examples and discuss optimal practices for these analytical tasks.
- To guide researchers in effectively utilizing ATAC-seq data.
Main Methods:
- Data processing and quality control of raw ATAC-seq reads.
- Peak calling to identify accessible chromatin regions.
- Differential accessibility analysis to find significant changes in chromatin accessibility.
- Analysis of transcription factor (TF) motif accessibility.
Main Results:
- Standardized computational pipelines are essential for robust ATAC-seq analysis.
- Key steps include data preprocessing, quality assessment, peak identification, and differential analysis.
- Understanding TF motif accessibility provides insights into gene regulation.
Conclusions:
- ATAC-seq is a versatile and adaptable assay for chromatin accessibility studies.
- Adherence to recommended analytical practices ensures reliable and reproducible results.
- This review serves as a guide for researchers analyzing ATAC-seq data.
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Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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