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

  • Author Footnotes
    1 MK is currently affiliated with the Department of Biological Sciences, Fordham University, Bronx, New York.
    ,
    Author Footnotes
    2 MK and YJ contributed equally to this work.
    Marija Kundakovic
    Footnotes
    1 MK is currently affiliated with the Department of Biological Sciences, Fordham University, Bronx, New York.
    2 MK and YJ contributed equally to this work.
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Author Footnotes
    2 MK and YJ contributed equally to this work.
    Yan Jiang
    Footnotes
    2 MK and YJ contributed equally to this work.
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • David H. Kavanagh
    Affiliations
    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
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  • Aslihan Dincer
    Affiliations
    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
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  • Leanne Brown
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Venu Pothula
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Elizabeth Zharovsky
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Royce Park
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Rivka Jacobov
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Isabelle Magro
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Bibi Kassim
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Jennifer Wiseman
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Kristen Dang
    Affiliations
    Sage Bionetworks, Seattle, Washington
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  • Solveig K. Sieberts
    Affiliations
    Sage Bionetworks, Seattle, Washington
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  • Panos Roussos
    Affiliations
    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
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  • Menachem Fromer
    Affiliations
    Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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  • Brent Harris
    Affiliations
    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
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  • Barbara K. Lipska
    Affiliations
    Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
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  • Mette A. Peters
    Affiliations
    Sage Bionetworks, Seattle, Washington
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  • Author Footnotes
    3 PS and SA are joint senior authors.
    Pamela Sklar
    Footnotes
    3 PS and SA are joint senior authors.
    Affiliations
    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
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  • Author Footnotes
    3 PS and SA are joint senior authors.
    Schahram Akbarian
    Correspondence
    Address correspondence to Schahram Akbarian, M.D., Ph.D., Mount Sinai School of Medicine, Psychiatry and Neuroscience, 1470 Madison Avenue, Hess CSM Room 9-105, New York, NY 10029.
    Footnotes
    3 PS and SA are joint senior authors.
    Affiliations
    Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
    Search for articles by this author
  • Author Footnotes
    1 MK is currently affiliated with the Department of Biological Sciences, Fordham University, Bronx, New York.
    2 MK and YJ contributed equally to this work.
    3 PS and SA are joint senior authors.

      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

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      Linked Article

      • Profiling Regulatory Variation in the Brain: Methods for Exploring the Neuronal Epigenome
        Biological PsychiatryVol. 81Issue 2
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          Epigenomic processes—acting to developmentally regulate gene expression via modifications to DNA, histone proteins, and chromatin—play a critical role in determining cell type–specific patterns of gene regulation in the human brain. By interacting with the milieu of transcription factors in each cell, for example, they orchestrate the complex changes in gene expression involved in neurodevelopment, and widespread changes in epigenetic modifications have been shown to occur during brain development (1).
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