Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome

Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 ref...

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Published inNature neuroscience Vol. 21; no. 8; pp. 1126 - 1136
Main Authors Girdhar, Kiran, Hoffman, Gabriel E., Jiang, Yan, Brown, Leanne, Kundakovic, Marija, Hauberg, Mads E., Francoeur, Nancy J., Wang, Ying-chih, Shah, Hardik, Kavanagh, David H., Zharovsky, Elizabeth, Jacobov, Rivka, Wiseman, Jennifer R., Park, Royce, Johnson, Jessica S., Kassim, Bibi S., Sloofman, Laura, Mattei, Eugenio, Weng, Zhiping, Sieberts, Solveig K., Peters, Mette A., Harris, Brent T., Lipska, Barbara K., Sklar, Pamela, Roussos, Panos, Akbarian, Schahram
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.08.2018
Nature Publishing Group
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Abstract Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe. This PsychENCODE resource presents 157 reference maps for open-chromatin-associated histone methylation and acetylation in prefrontal and anterior cingulate cortex, linking the neuronal epigenome to the genetic risk architecture of schizophrenia.
AbstractList Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe.Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe.
Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe.
Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe. This PsychENCODE resource presents 157 reference maps for open-chromatin-associated histone methylation and acetylation in prefrontal and anterior cingulate cortex, linking the neuronal epigenome to the genetic risk architecture of schizophrenia.
Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe. This PsychENCODE resource presents 157 reference maps for open-chromatin-associated histone methylation and acetylation in prefrontal and anterior cingulate cortex, linking the neuronal epigenome to the genetic risk architecture of schizophrenia.
Audience Academic
Author Kundakovic, Marija
Kavanagh, David H.
Zharovsky, Elizabeth
Brown, Leanne
Hauberg, Mads E.
Akbarian, Schahram
Girdhar, Kiran
Johnson, Jessica S.
Jiang, Yan
Wiseman, Jennifer R.
Lipska, Barbara K.
Mattei, Eugenio
Hoffman, Gabriel E.
Sloofman, Laura
Park, Royce
Harris, Brent T.
Roussos, Panos
Wang, Ying-chih
Kassim, Bibi S.
Weng, Zhiping
Jacobov, Rivka
Sieberts, Solveig K.
Peters, Mette A.
Shah, Hardik
Sklar, Pamela
Francoeur, Nancy J.
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  organization: Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/30038276$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright The Author(s) 2018
COPYRIGHT 2018 Nature Publishing Group
Copyright Nature Publishing Group Aug 2018
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– notice: COPYRIGHT 2018 Nature Publishing Group
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Snippet Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly...
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SubjectTerms 45
45/15
45/23
631/114/1314
692/699/476/1799
Alzheimer Disease - genetics
Animal Genetics and Genomics
Behavioral Sciences
Biological Techniques
Biomedical and Life Sciences
Biomedicine
Brain
Brain Mapping
Brain research
Chromatin
Chromatin - genetics
Corporate sponsorship
Cortex (cingulate)
Depletion
Depression - genetics
Depression - pathology
Educational Status
Enhancers
Epigenesis, Genetic - genetics
Epigenetic inheritance
Frontal lobe
Frontal Lobe - metabolism
Frontal Lobe - pathology
Frontal lobes
Gene mapping
Genetic aspects
Genetic Predisposition to Disease - genetics
Genetic Variation
Genome-Wide Association Study
Gyrus Cinguli - pathology
Health aspects
Histones
Histones - genetics
Humans
Landscape
Legal liability
Liability
Medical schools
Mental disorders
Methylation
Molecular neurobiology
Neurobiology
Neurogenetics
Neurons
Neurosciences
Neurosis
Neurotic Disorders - genetics
Neurotic Disorders - pathology
Physiological aspects
Post-translational modifications
Prefrontal cortex
Prefrontal Cortex - pathology
Psychosis
Quantitative genetics
Quantitative trait loci
Resource
Risk
Risk factors
Schizophrenia
Schizophrenia - genetics
Schizophrenia - metabolism
Title Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome
URI https://link.springer.com/article/10.1038/s41593-018-0187-0
https://www.ncbi.nlm.nih.gov/pubmed/30038276
https://www.proquest.com/docview/2076903731
https://www.proquest.com/docview/2075547009
Volume 21
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