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

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• 作者：Marija Kundakovic^a ; ¹ ; ² ; Yan Jiang^a ; ² ; David H. Kavanagh^a ; ^b ; Aslihan Dincer^a ; ^b ; Leanne Brown^a ; Venu Pothula^a ; Elizabeth Zharovsky^a ; Royce Park^a ; Rivka Jacobov^a ; Isabelle Magro^a ; Bibi Kassim^a ; Jennifer Wiseman^a ; Kristen Dang^c ; Solveig K. Sieberts^c ; Panos Roussos^a ; ^b ; Menachem Fromer^b ; Brent Harris^d ; ^e ; Barbara K. Lipska^e ; Mette A. Peters^c ; Pamela Sklar^a ; ^b ; ³ ; Schahram Akbarian^a ; ³ ; ^{Schahram.akbarian@mssm.edu}
• 关键词：Cell type specific ; ChIP-seq ; Epigenomics ; Postmortem human brain ; PsychENCODE ; Schizophrenia
• 刊名：Biological Psychiatry
• 出版年：2017
• 出版时间：15 January 2017
• 年：2017
• 卷：81
• 期：2
• 页码：162-170
• 全文大小：1208 K
• 卷排序：81

文摘

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.MethodsProtocols 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.ResultsWe 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.ConclusionsOur 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.