Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq

Georgi K Marinov; Zohar Shipony; Anshul Kundaje; William J Greenleaf

doi:10.1007/978-1-0716-2899-7_1

Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq

Methods Mol Biol. 2023:2611:3-19. doi: 10.1007/978-1-0716-2899-7_1.

Authors

Georgi K Marinov¹, Zohar Shipony², Anshul Kundaje^{2

3}, William J Greenleaf^{4

5

6

7}

Affiliations

¹ Department of Genetics, Stanford University, Stanford, CA, USA. marinovg@stanford.edu.
² Department of Genetics, Stanford University, Stanford, CA, USA.
³ Department of Computer Science, Stanford University, Stanford, CA, USA.
⁴ Department of Genetics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
⁵ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
⁶ Department of Applied Physics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
⁷ Chan Zuckerberg Biohub, San Francisco, CA, USA. wjg@stanford.edu.

PMID: 36807060
DOI: 10.1007/978-1-0716-2899-7_1

Abstract

Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs genome-wide and tracking their dynamics across different cellular states and is the basis of numerous methods taking advantage of the preferential enzymatic cleavage/labeling of accessible DNA. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) has emerged as the most versatile and widely adaptable method and has been widely adopted as the standard tool for mapping open chromatin regions. Here, we discuss the current optimal practices and important considerations for carrying out ATAC-seq experiments, primarily in the context of mammalian systems.

Keywords: ATAC-seq; Chromatin accessibility; Enhancers; High-throughput sequencing; Promoters.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromatin
Chromatin Immunoprecipitation Sequencing*
High-Throughput Nucleotide Sequencing*
Mammals / genetics
Regulatory Sequences, Nucleic Acid
Sequence Analysis, DNA

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding