Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Noga Korenfeld; Nicolaj I. Toft; Trine V. Dam; Meital Charni-Natan; Lars Grøntved; Ido Goldstein

doi:10.1016/j.xpro.2023.102462

Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Noga Korenfeld, Nicolaj I. Toft, Trine V. Dam, Meital Charni-Natan, Lars Grøntved^*, Ido Goldstein^*

^*Corresponding author for this work

Institute of Biochemistry, Food Science and Nutrition

Research output: Contribution to journal › Article › peer-review

Abstract

The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.

Original language	American English
Article number	102462
Journal	STAR Protocols
Volume	4
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2023.102462
State	Published - 15 Sep 2023

Bibliographical note

Funding Information:
The methodology development in the Grøntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant # 141 ). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907 ), the Israel Science Foundation (ISF, grants numbers 1469/19 , 3533/19 ), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing.

Funding Information:
The methodology development in the Grøntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant #141). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907), the Israel Science Foundation (ISF, grants numbers 1469/19, 3533/19), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. N.K. and N.I.T. developed and optimized the method and wrote the manuscript. T.V.D. and M.C-N. developed and optimized the method. L.G. and I.G. developed the method, acquired funding, supervised the project, and wrote the manuscript. The authors declare no competing interests.

Publisher Copyright:
© 2023 The Author(s)

Keywords

Genomics
Metabolism
Molecular Biology
Single Cell

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10.1016/j.xpro.2023.102462

Cite this

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title = "Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue",

abstract = "The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR amplification, and pre- and post-sequencing quality control. Our protocol is optimized for the liver, a tissue where nuclei isolation requires distinct steps. We provide two detailed vignettes: one for bulk ATAC-seq and another for single-nuclei ATAC-seq.",

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note = "Funding Information: The methodology development in the Gr{\o}ntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant # 141 ). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907 ), the Israel Science Foundation (ISF, grants numbers 1469/19 , 3533/19 ), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. Funding Information: The methodology development in the Gr{\o}ntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant #141). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907), the Israel Science Foundation (ISF, grants numbers 1469/19, 3533/19), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. N.K. and N.I.T. developed and optimized the method and wrote the manuscript. T.V.D. and M.C-N. developed and optimized the method. L.G. and I.G. developed the method, acquired funding, supervised the project, and wrote the manuscript. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2023 The Author(s)",

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AU - Charni-Natan, Meital

AU - Grøntved, Lars

AU - Goldstein, Ido

N1 - Funding Information: The methodology development in the Grøntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant # 141 ). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907 ), the Israel Science Foundation (ISF, grants numbers 1469/19 , 3533/19 ), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. Funding Information: The methodology development in the Grøntved lab was supported by the ATLAS center of excellence supported by a grant from the Danish National Research Foundation (grant #141). Work in the Goldstein lab was supported by the European Research Council (ERC-StG grant number 947907), the Israel Science Foundation (ISF, grants numbers 1469/19, 3533/19), the Canadian Institutes of Health Research (CIHR), and the International Development Research Centre (IDRC). We would like to thank Dr. Abed Nasereddin and Dr. Idit Shiff from the Genomic Applications Lab, Hebrew University of Jerusalem, and Ronni Nielsen from the Department of Biochemistry and Molecular Biology, University of Southern Denmark, for their invaluable help, support, and expertise in high-throughput sequencing. N.K. and N.I.T. developed and optimized the method and wrote the manuscript. T.V.D. and M.C-N. developed and optimized the method. L.G. and I.G. developed the method, acquired funding, supervised the project, and wrote the manuscript. The authors declare no competing interests. Publisher Copyright: © 2023 The Author(s)

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KW - Metabolism

KW - Molecular Biology

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JO - STAR Protocols

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ER -

Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue

Abstract

Bibliographical note

Keywords

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