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



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.



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.



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.
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Marija
M
Kundakovic
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Yan
Y
Jiang
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.
David H
DH
Kavanagh
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.
Aslihan
A
Dincer
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Leanne
L
Brown
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Venu
V
Pothula
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Elizabeth
E
Zharovsky
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Royce
R
Park
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Rivka
R
Jacobov
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Isabelle
I
Magro
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Bibi
B
Kassim
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
Jennifer
J
Wiseman
Sage Bionetworks, Seattle, Washington.
Kristen
K
Dang
Sage Bionetworks, Seattle, Washington.
Solveig K
SK
Sieberts
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.
Panos
P
Roussos
Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
Menachem
M
Fromer
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.
Brent
B
Harris
Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland.
Barbara K
BK
Lipska
Sage Bionetworks, Seattle, Washington.
Mette A
MA
Peters
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.
Pamela
P
Sklar
Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York. Electronic address: Schahram.akbarian@mssm.edu.
Schahram
S
Akbarian
D000107:Acetylation; D034961:Antigens, Nuclear / Q000378:metabolism; D002540:Cerebral Cortex / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006657:Histones / Q000378:metabolism*; D006801:Humans; D008745:Methylation; D009419:Nerve Tissue Proteins / Q000378:metabolism; D009474:Neurons / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011499:Protein Processing, Post-Translational
D034961:Antigens, Nuclear; D006657:Histones; D009419:Nerve Tissue Proteins; D009707:Nucleosomes; C506808:neuronal nuclear antigen NeuN, human
Cell type specific; ChIP-seq; Epigenomics; Postmortem human brain; PsychENCODE; Schizophrenia