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Biol Psychiatry. 2017 Jan 15;81(2):162-170. doi: 10.1016/j.biopsych.2016.03.1048. Epub 2016 Mar 9.

Practical Guidelines for High-Resolution Epigenomic Profiling of Nucleosomal Histones in Postmortem Human Brain Tissue.

Author information

1
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
2
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
3
Sage Bionetworks, Seattle, Washington.
4
Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
5
Department of Neurology, Georgetown University Medical Center, Washington, DC; Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland.
6
Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland.
7
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York. Electronic address: Schahram.akbarian@mssm.edu.

Abstract

BACKGROUND:

The nervous system may include more than 100 residue-specific posttranslational modifications of histones forming the nucleosome core that are often regulated in cell-type-specific manner. On a genome-wide scale, some of the histone posttranslational modification landscapes show significant overlap with the genetic risk architecture for several psychiatric disorders, fueling PsychENCODE and other large-scale efforts to comprehensively map neuronal and nonneuronal epigenomes in hundreds of specimens. However, practical guidelines for efficient generation of histone chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) datasets from postmortem brains are needed.

METHODS:

Protocols and quality controls are given for the following: 1) extraction, purification, and NeuN neuronal marker immunotagging of nuclei from adult human cerebral cortex; 2) fluorescence-activated nuclei sorting; 3) preparation of chromatin by micrococcal nuclease digest; 4) ChIP for open chromatin-associated histone methylation and acetylation; and 5) generation and sequencing of ChIP-seq libraries.

RESULTS:

We present a ChIP-seq pipeline for epigenome mapping in the neuronal and nonneuronal nuclei from the postmortem brain. This includes a stepwise system of quality controls and user-friendly data presentation platforms.

CONCLUSIONS:

Our practical guidelines will be useful for projects aimed at histone posttranslational modification mapping in chromatin extracted from hundreds of postmortem brain samples in cell-type-specific manner.

KEYWORDS:

Cell type specific; ChIP-seq; Epigenomics; Postmortem human brain; PsychENCODE; Schizophrenia

PMID:
27113501
PMCID:
PMC5017897
DOI:
10.1016/j.biopsych.2016.03.1048
[Indexed for MEDLINE]
Free PMC Article

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