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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
Published on: November 13, 2017
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Genome-wide analysis of chromatin accessibility using ATAC-seq
Tanvi Shashikant1, Charles A Ettensohn1
1Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
Methods in Cell Biology
|April 6, 2019
Summary
This study details a protocol for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in sea urchin embryos. This method identifies regulatory DNA elements controlling gene transcription by mapping open chromatin regions.
Area of Science:
- Molecular Biology
- Genomics
- Developmental Biology
Background:
- Gene transcription is regulated by cis-acting DNA elements like enhancers and promoters.
- Chromatin accessibility is a key structural feature for identifying these regulatory elements.
- Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a powerful technique for genome-wide chromatin accessibility profiling.
Purpose of the Study:
- To present a detailed protocol for applying ATAC-seq to sea urchin embryonic cells.
- To enable the study of genomic control of animal development using ATAC-seq in echinoderm models.
Main Methods:
- Utilizes hyperactive Tn5 transposase to cut and tag accessible DNA regions.
- Assesses genome-wide chromatin accessibility.
- Adapted for use with a small number of cells, suitable for developing embryos.
Main Results:
- The protocol is effective for profiling chromatin accessibility in sea urchin embryonic cells.
- Identifies open chromatin regions indicative of regulatory elements.
- Provides a foundation for understanding gene regulation in sea urchin development.
Conclusions:
- ATAC-seq is a feasible and powerful method for studying gene regulation in sea urchin embryos.
- This protocol facilitates research into the genomic control of developmental processes in echinoderms.
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