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 in | Nature neuroscience Vol. 21; no. 8; pp. 1126 - 1136 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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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. |
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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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Institute, Icahn School of Medicine at Mount Sinai, Department of Biological Sciences, Fordham University – sequence: 6 givenname: Mads E. orcidid: 0000-0003-4873-2764 surname: Hauberg fullname: Hauberg, Mads E. organization: iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Department of Biomedicine, Aarhus University – sequence: 7 givenname: Nancy J. surname: Francoeur fullname: Francoeur, Nancy J. organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai – sequence: 8 givenname: Ying-chih surname: Wang fullname: Wang, Ying-chih organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai – sequence: 9 givenname: Hardik surname: Shah fullname: Shah, Hardik organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai – 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Jessica S. surname: Johnson fullname: Johnson, Jessica S. organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai – sequence: 16 givenname: Bibi S. surname: Kassim fullname: Kassim, Bibi S. organization: Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai – sequence: 17 givenname: Laura surname: Sloofman fullname: Sloofman, Laura organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai – sequence: 18 givenname: Eugenio orcidid: 0000-0002-8889-658X surname: Mattei fullname: Mattei, Eugenio organization: Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School – sequence: 19 givenname: Zhiping orcidid: 0000-0002-3032-7966 surname: Weng fullname: Weng, Zhiping organization: Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School – sequence: 20 givenname: Solveig K. orcidid: 0000-0003-1033-0954 surname: Sieberts fullname: Sieberts, Solveig K. organization: Systems Biology, Sage Bionetworks – sequence: 21 givenname: Mette A. surname: Peters fullname: Peters, Mette A. organization: Systems Biology, Sage Bionetworks – sequence: 22 givenname: Brent T. surname: Harris fullname: Harris, Brent T. organization: Department of Neurology, Georgetown University, Human Brain Collection Core, NIMH – sequence: 23 givenname: Barbara K. surname: Lipska fullname: Lipska, Barbara K. organization: Human Brain Collection Core, NIMH – sequence: 24 givenname: Pamela surname: Sklar fullname: Sklar, Pamela organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai – sequence: 25 givenname: Panos orcidid: 0000-0002-4640-6239 surname: Roussos fullname: Roussos, Panos email: panagiotis.roussos@mssm.edu organization: Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Mental Illness Research, Education, and Clinical Center, James J. Peters VA Medical Center – sequence: 26 givenname: Schahram orcidid: 0000-0001-7700-0891 surname: Akbarian fullname: Akbarian, Schahram email: schahram.akbarian@mssm.edu organization: Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30038276$$D View this record in MEDLINE/PubMed |
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Title | Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome |
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