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

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Skeletal Muscle Stem Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2640))

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.

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Acknowledgments

This work was supported by the Excellence Initiative “Cardiopulmonary Institute” (CPI), the DFG collaborative research center SFB1213, the DFG Transregional Collaborative Research Centre 81, the DFG Clinical Research Unit FKO 309, and the European Research Area Network on Cardiovascular Diseases project CLARIFY.

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Authors and Affiliations

  1. Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany

    Michail Yekelchyk, Stefan Guenther & Thomas Braun

  2. German Centre for Cardiovascular Research (DZHK), Partner site Rhein-Main, Frankfurt am Main, Germany

    Michail Yekelchyk, Stefan Guenther & Thomas Braun

Authors
  1. Michail Yekelchyk
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  2. Stefan Guenther
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  3. Thomas Braun
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Corresponding author

Correspondence to Thomas Braun .

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Editors and Affiliations

  1. Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA

    Atsushi Asakura

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Yekelchyk, M., Guenther, S., Braun, T. (2023). Assay for Transposase-Accessible Chromatin Using Sequencing of Freshly Isolated Muscle Stem Cells. In: Asakura, A. (eds) Skeletal Muscle Stem Cells. Methods in Molecular Biology, vol 2640. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3036-5_27

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  • DOI: https://doi.org/10.1007/978-1-0716-3036-5_27

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3035-8

  • Online ISBN: 978-1-0716-3036-5

  • eBook Packages: Springer Protocols

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