FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C

Ekaterina Eremenko; Anastasia Golova; Daniel Stein; Monica Einav; Ekaterina Khrameeva; Debra Toiber

doi:10.1016/j.xpro.2021.100643

FACS-based isolation of fixed mouse neuronal nuclei for ATAC-seq and Hi-C

STAR Protoc. 2021 Jul 9;2(3):100643. doi: 10.1016/j.xpro.2021.100643. eCollection 2021 Sep 17.

Authors

Ekaterina Eremenko^{1

2}, Anastasia Golova³, Daniel Stein^{1

2}, Monica Einav^{1

2}, Ekaterina Khrameeva³, Debra Toiber^{1

2}

Affiliations

¹ Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
² The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
³ Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.

Abstract

The organization of chromatin structure plays a crucial role in gene expression, DNA replication, and repair. Chromatin alterations influence gene expression, and modifications could be associated with genomic instability in the cells during aging or diseases. Here, we provide a modified protocol to isolate fixed neuronal nuclei from a single mouse cortex to investigate the spatial organization of chromatin structure on a genome-wide scale by ATAC-seq (the assay for transposase-accessible chromatin with high-throughput sequencing) and chromatin conformation by Hi-C (high-throughput chromosome conformation capture).

Keywords: Cell Biology; Cell separation/fractionation; Flow Cytometry/Mass Cytometry; Genomics; Neuroscience.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cell Nucleus / genetics*
Chromatin / genetics*
Chromatin Immunoprecipitation Sequencing / methods*
Flow Cytometry / methods*
High-Throughput Nucleotide Sequencing / methods
Mice
Mice, Inbred C57BL
Neurons / cytology*
Neurons / physiology
Polymerase Chain Reaction
Transposases

Substances

Chromatin
Transposases