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Updated: Nov 11, 2025

A Chromatin Assay for Human Brain Tissue

A Chromatin Assay for Human Brain Tissue

Published on: March 21, 2008

Cell type-specific chromatin accessibility analysis in the mouse and human brain.

Devin Rocks¹, Ivana Jaric¹, Lydia Tesfa²

¹Department of Biological Sciences, Fordham University, Bronx, NY, USA.

|March 29, 2021

Summary

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We evaluated brain tissue freezing methods for Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) in neuroscience. Different freezing methods impact open chromatin region counts but do not alter broad biological interpretations.

Area of Science:

Neuroscience
Genomics
Epigenetics

Background:

Chromatin regulation is crucial in neurodevelopment and neuropsychiatric disorders.
Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is a valuable tool for studying gene regulatory elements.
Standardized protocols are needed for reliable chromatin accessibility analysis in neuroscience.

Purpose of the Study:

To evaluate the impact of different brain tissue cryopreservation methods on ATAC-seq data quality.
To assess the compatibility of various protocols with fluorescence-activated nuclei sorting (FANS) for neuronal chromatin analysis.
To provide guidance on selecting appropriate preservation methods for neuroscience studies using ATAC-seq.

Main Methods:

Tested three protocols for neuronal chromatin accessibility analysis.

Keywords:

ATAC-seq Chromatin accessibility FACS cell type-specific epigenomics freezing method human brain mouse brain neuron

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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

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Last Updated: Nov 11, 2025

A Chromatin Assay for Human Brain Tissue

A Chromatin Assay for Human Brain Tissue

Published on: March 21, 2008

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Published on: January 23, 2019

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

Included varying brain tissue freezing methods.

Utilized fluorescence-activated nuclei sorting (FANS) coupled with ATAC-seq.

Main Results:

Cryopreservation methods influence the number of open chromatin regions detected by ATAC-seq.
All tested protocols yield consistent and robust data for identifying functional regulatory elements.
Broad biological interpretations of chromatin accessibility data remain largely unaffected by freezing conditions.

Conclusions:

ATAC-seq combined with FANS is effective for cell-type-specific chromatin accessibility analysis in mouse and human brains.
The study offers alternative brain preservation methods suitable for diverse study designs.
This work encourages further exploration of epigenetic regulation in brain function and disease using ATAC-seq.