Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023:2640:397-412.
doi: 10.1007/978-1-0716-3036-5_27.

Assay for Transposase-Accessible Chromatin Using Sequencing of Freshly Isolated Muscle Stem Cells

Michail Yekelchyk  1   2 , Stefan Guenther  1   2 , Thomas Braun  3   4
Affiliations

Assay for Transposase-Accessible Chromatin Using Sequencing of Freshly Isolated Muscle Stem Cells

Michail Yekelchyk et al. Methods Mol Biol. 2023.

Abstract

Actively transcribed genes harbor cis-regulatory modules with comparatively low nucleosome occupancy and few high-order structures (="open chromatin"), whereas non-transcribed genes are characterized by high nucleosome density and extensive interactions between nucleosomes (="closed chromatin"), preventing transcription factor binding. Knowledge about chromatin accessibility is crucial to understand gene regulatory networks determining cellular decisions. Several techniques are available to map chromatin accessibility, among which the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is one of the most popular. ATAC-seq is based on a straightforward and robust protocol but requires adjustments for different cell types. Here, we describe an optimized protocol for ATAC-seq of freshly isolated murine muscle stem cells. We provide details for the isolation of MuSC, tagmentation, library amplification, double-sided SPRI bead cleanup, and library quality assessment and give recommendations for sequencing parameters and downstream analysis. The protocol should facilitate generation of high-quality data sets of chromatin accessibility in MuSCs, even for newcomers to the field.

Keywords: ATAC-seq; Chromatin accessibility; Muscle stem cells; NGS; Satellite cells; Sequencing; Transposase.

PubMed Disclaimer

Similar articles

See all similar articles

References

    1. Mayran A, Drouin J (2018) Pioneer transcription factors shape the epigenetic landscape. J Biol Chem 293(36):13795–13804. https://doi.org/10.1074/jbc.R117.001232 - DOI - PubMed - PMC
    1. Klemm SL, Shipony Z, Greenleaf WJ (2019) Chromatin accessibility and the regulatory epigenome. Nat Rev Genet 20(4):207–220. https://doi.org/10.1038/s41576-018-0089-8 - DOI - PubMed
    1. Buenrostro JD, Wu B, Chang HY et al (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109:21 29 21-21 29 29. https://doi.org/10.1002/0471142727.mb2129s109 - DOI
    1. Jia G, Preussner J, Chen X et al (2018) Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement. Nat Commun 9(1):4877. https://doi.org/10.1038/s41467-018-07307-6 - DOI - PubMed - PMC
    1. Ludwig LS, Lareau CA, Bao EL et al (2019) Transcriptional states and chromatin accessibility underlying human erythropoiesis. Cell Rep 27(11):3228–3240 e3227. https://doi.org/10.1016/j.celrep.2019.05.046 - DOI - PubMed - PMC

Publication types

LinkOut - more resources