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

STAR Protoc. 2023 Sep 15;4(3):102462. doi: 10.1016/j.xpro.2023.102462. Epub 2023 Aug 16.

Authors

Noga Korenfeld¹, Nicolaj I Toft², Trine V Dam², Meital Charni-Natan¹, Lars Grøntved³, Ido Goldstein⁴

Affiliations

¹ Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel.
² Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
³ Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark. Electronic address: larsgr@bmb.sdu.dk.
⁴ Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel. Electronic address: ido.goldstein@mail.huji.ac.il.

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.

Keywords: Genomics; Metabolism; Molecular Biology; Single Cell.

MeSH terms

Animals
Cell Nucleus / genetics
Chromatin Immunoprecipitation Sequencing
Chromatin* / genetics
High-Throughput Nucleotide Sequencing* / methods
Mice
Sequence Analysis, DNA / methods

Substances

Chromatin