Exploring Chromatin Accessibility in Mouse Epiblast Stem Cells with ATAC-Seq

Nazmus Salehin; Nicole Santucci; Pierre Osteil; Patrick P L Tam

doi:10.1007/978-1-0716-2281-0_9

Exploring Chromatin Accessibility in Mouse Epiblast Stem Cells with ATAC-Seq

Methods Mol Biol. 2022:2490:93-100. doi: 10.1007/978-1-0716-2281-0_9.

Authors

Nazmus Salehin^{1

2}, Nicole Santucci³, Pierre Osteil^{3

4

5}, Patrick P L Tam^{3

4}

Affiliations

¹ Embryology Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia. nsalehin@cmri.org.au.
² Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia. nsalehin@cmri.org.au.
³ Embryology Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia.
⁴ Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
⁵ Swiss Cancer Research Institute (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

PMID: 35486242
DOI: 10.1007/978-1-0716-2281-0_9

Abstract

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is used to identify open chromatin regions in cells. This can be used to identify putative regulatory regions, determine dynamics and mechanisms of transcription factors when coupled with ChIP-seq and predict interactions between proteins and chromatin. Compared to previous methods, MNase-seq and DNase-seq, ATAC-seq requires only 50,000 cells, orders of magnitude fewer cells. In addition, the ATAC-seq protocol takes one day to progress from cells to sequencing ready libraries.

Keywords: ATAC-seq; Accessibility; Chromatin; EpiSC.

MeSH terms

Animals
Chromatin Immunoprecipitation Sequencing*
Chromatin* / genetics
Germ Layers
High-Throughput Nucleotide Sequencing / methods
Mice
Stem Cells

Substances

Chromatin