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Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders.

Arloth J, Bogdan R, Weber P, Frishman G, Menke A, Wagner KV, Balsevich G, Schmidt MV, Karbalai N, Czamara D, Altmann A, Trümbach D, Wurst W, Mehta D, Uhr M, Klengel T, Erhardt A, Carey CE, Conley ED, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (PGC)Ruepp A, Müller-Myhsok B, Hariri AR, Binder EB, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium P - Neuron (2015)

Bottom Line: One putative biological mechanism implicates variability in the ability of cortisol, released in response to stress, to trigger a cascade of adaptive genomic and non-genomic processes through glucocorticoid receptor (GR) activation.Here, we demonstrate that common genetic variants in long-range enhancer elements modulate the immediate transcriptional response to GR activation in human blood cells.Moreover, these risk variants are associated with inappropriate amygdala reactivity, a transdiagnostic psychiatric endophenotype and an important stress hormone response trigger.

View Article: PubMed Central - PubMed

Affiliation: Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany.

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Related in: MedlinePlus

Long-Range Chromatin Interaction of GR-Response eQTLs(A) Long-range chromatin interaction as exemplified by the eSNP region containing the NRTN locus (chr10: 5,690,000–5,840,000; hg19) was confirmed by 3C in five lymphoblastoid cell lines (LCLs) each, homozygous for the two opposite SNP alleles, both in the presence and absence of dexamethasone. A SNP in the NRTN locus (rs1379868) affects the differentially regulated gene expression of LONP1 in human whole blood cells (based on GR-response eQTL analysis). Baseline (6 p.m.) measures are displayed in blue and GR-stimulated measures (9 p.m.) in red.(B) SNP effect on GR-dependent gene transcription was validated by qPCR in the LCLs used for the 3C assay.(C) Characterization of the eSNP locus. Top panel, ideogram for chromosome 19 (p13.3). A red box isolates the region shown (enlarged) in the bottom panel. Bottom panel: 3C-primers (green track) were designed at the LONP1 TSS (C1, anchor) and multiple regions (P1–P6) in and around the eSNP bin. The eSNP bin includes a GR binding site in blood cells (pink track). ChIA-PET tags from the leukemia cell line (brown and green tracks) validate a direct chromatin interaction between the NRTN eSNP locus and the regulated gene LONP1. The paired ChIA-PET tags coincide with DNaseI hypersensitivity sites in the leukemia cell line (red track) and blood cells (yellow track).(D) Chromatin conformation capture interaction data. A 3C physical interaction between the LONP1 TSS and eSNP bin (P4), emphasized by a gray box, was found in the 3C libraries made from LCLs (p = 3.35 × 10−23, χ2 = 115.15) with a stronger interaction following stimulation with the GR-agonist (p = 0.06, χ2 = 3.35). Q values in (A) are derived from GR-response cis-eQTL analysis, and p values in (B) and (D) are derived from linear mixed model; error bars ± SD.
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fig4: Long-Range Chromatin Interaction of GR-Response eQTLs(A) Long-range chromatin interaction as exemplified by the eSNP region containing the NRTN locus (chr10: 5,690,000–5,840,000; hg19) was confirmed by 3C in five lymphoblastoid cell lines (LCLs) each, homozygous for the two opposite SNP alleles, both in the presence and absence of dexamethasone. A SNP in the NRTN locus (rs1379868) affects the differentially regulated gene expression of LONP1 in human whole blood cells (based on GR-response eQTL analysis). Baseline (6 p.m.) measures are displayed in blue and GR-stimulated measures (9 p.m.) in red.(B) SNP effect on GR-dependent gene transcription was validated by qPCR in the LCLs used for the 3C assay.(C) Characterization of the eSNP locus. Top panel, ideogram for chromosome 19 (p13.3). A red box isolates the region shown (enlarged) in the bottom panel. Bottom panel: 3C-primers (green track) were designed at the LONP1 TSS (C1, anchor) and multiple regions (P1–P6) in and around the eSNP bin. The eSNP bin includes a GR binding site in blood cells (pink track). ChIA-PET tags from the leukemia cell line (brown and green tracks) validate a direct chromatin interaction between the NRTN eSNP locus and the regulated gene LONP1. The paired ChIA-PET tags coincide with DNaseI hypersensitivity sites in the leukemia cell line (red track) and blood cells (yellow track).(D) Chromatin conformation capture interaction data. A 3C physical interaction between the LONP1 TSS and eSNP bin (P4), emphasized by a gray box, was found in the 3C libraries made from LCLs (p = 3.35 × 10−23, χ2 = 115.15) with a stronger interaction following stimulation with the GR-agonist (p = 0.06, χ2 = 3.35). Q values in (A) are derived from GR-response cis-eQTL analysis, and p values in (B) and (D) are derived from linear mixed model; error bars ± SD.

Mentions: To evaluate whether the long-range regulation of GR-response eQTLs may be associated with long-range physical chromatin interaction, we compared our data with that from a chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) generated by ENCODE (ENCODE Project Consortium, 2011) in the leukemia cell line K562. For this, we examined whether regions containing the GR-response eSNP bin and the corresponding probe gene overlap with physically interacting ChIA-PET tags (see Experimental Procedures). Twenty-five percent of the GR-response eSNP bin-probe gene combinations overlapped with chromatin interaction signals. This was significantly greater than 1,000 equally sized sets of randomly distributed GR-response eSNP bin, especially when restricting the analysis to more long-range eSNP bin-probe gene pairs with distances > 100 kb (fold enrichment>100kb = 1.57, permutation-based FDR>100kb = 0.007; see Experimental Procedures). To validate these long-range chromatin interactions, we used a chromatin conformation capture (3C) assay to confirm a physical interaction between the eSNP bin regions of the GR-response eSNP tag rs1379868 in the NRTN locus and the corresponding GR-stimulated transcript LONP1 (see Figures 4A and 4B), which is over 130 kb upstream. This eSNP bin includes a GR binding site and ChIA-PET tags (see Figure 4C), which interact with the transcription start site of the LONP1 gene. The 3C assay confirmed an increased chromatin interaction (p = 3.35 × 10−23, χ2 = 115.15 at baseline) of the eSNP bin with the TSS of the LONP1 gene (P4 in Figures 4C and 4D) in five LCLs. The average interaction frequency of these two sites was higher following stimulation with the GR-agonist dexamethasone (4.83 versus 5.65). These results suggest that long-range regulation of GR-response eQTLs could be mediated by direct chromatin interaction of enhancer regions with the respective transcription start sites.


Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders.

Arloth J, Bogdan R, Weber P, Frishman G, Menke A, Wagner KV, Balsevich G, Schmidt MV, Karbalai N, Czamara D, Altmann A, Trümbach D, Wurst W, Mehta D, Uhr M, Klengel T, Erhardt A, Carey CE, Conley ED, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (PGC)Ruepp A, Müller-Myhsok B, Hariri AR, Binder EB, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium P - Neuron (2015)

Long-Range Chromatin Interaction of GR-Response eQTLs(A) Long-range chromatin interaction as exemplified by the eSNP region containing the NRTN locus (chr10: 5,690,000–5,840,000; hg19) was confirmed by 3C in five lymphoblastoid cell lines (LCLs) each, homozygous for the two opposite SNP alleles, both in the presence and absence of dexamethasone. A SNP in the NRTN locus (rs1379868) affects the differentially regulated gene expression of LONP1 in human whole blood cells (based on GR-response eQTL analysis). Baseline (6 p.m.) measures are displayed in blue and GR-stimulated measures (9 p.m.) in red.(B) SNP effect on GR-dependent gene transcription was validated by qPCR in the LCLs used for the 3C assay.(C) Characterization of the eSNP locus. Top panel, ideogram for chromosome 19 (p13.3). A red box isolates the region shown (enlarged) in the bottom panel. Bottom panel: 3C-primers (green track) were designed at the LONP1 TSS (C1, anchor) and multiple regions (P1–P6) in and around the eSNP bin. The eSNP bin includes a GR binding site in blood cells (pink track). ChIA-PET tags from the leukemia cell line (brown and green tracks) validate a direct chromatin interaction between the NRTN eSNP locus and the regulated gene LONP1. The paired ChIA-PET tags coincide with DNaseI hypersensitivity sites in the leukemia cell line (red track) and blood cells (yellow track).(D) Chromatin conformation capture interaction data. A 3C physical interaction between the LONP1 TSS and eSNP bin (P4), emphasized by a gray box, was found in the 3C libraries made from LCLs (p = 3.35 × 10−23, χ2 = 115.15) with a stronger interaction following stimulation with the GR-agonist (p = 0.06, χ2 = 3.35). Q values in (A) are derived from GR-response cis-eQTL analysis, and p values in (B) and (D) are derived from linear mixed model; error bars ± SD.
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fig4: Long-Range Chromatin Interaction of GR-Response eQTLs(A) Long-range chromatin interaction as exemplified by the eSNP region containing the NRTN locus (chr10: 5,690,000–5,840,000; hg19) was confirmed by 3C in five lymphoblastoid cell lines (LCLs) each, homozygous for the two opposite SNP alleles, both in the presence and absence of dexamethasone. A SNP in the NRTN locus (rs1379868) affects the differentially regulated gene expression of LONP1 in human whole blood cells (based on GR-response eQTL analysis). Baseline (6 p.m.) measures are displayed in blue and GR-stimulated measures (9 p.m.) in red.(B) SNP effect on GR-dependent gene transcription was validated by qPCR in the LCLs used for the 3C assay.(C) Characterization of the eSNP locus. Top panel, ideogram for chromosome 19 (p13.3). A red box isolates the region shown (enlarged) in the bottom panel. Bottom panel: 3C-primers (green track) were designed at the LONP1 TSS (C1, anchor) and multiple regions (P1–P6) in and around the eSNP bin. The eSNP bin includes a GR binding site in blood cells (pink track). ChIA-PET tags from the leukemia cell line (brown and green tracks) validate a direct chromatin interaction between the NRTN eSNP locus and the regulated gene LONP1. The paired ChIA-PET tags coincide with DNaseI hypersensitivity sites in the leukemia cell line (red track) and blood cells (yellow track).(D) Chromatin conformation capture interaction data. A 3C physical interaction between the LONP1 TSS and eSNP bin (P4), emphasized by a gray box, was found in the 3C libraries made from LCLs (p = 3.35 × 10−23, χ2 = 115.15) with a stronger interaction following stimulation with the GR-agonist (p = 0.06, χ2 = 3.35). Q values in (A) are derived from GR-response cis-eQTL analysis, and p values in (B) and (D) are derived from linear mixed model; error bars ± SD.
Mentions: To evaluate whether the long-range regulation of GR-response eQTLs may be associated with long-range physical chromatin interaction, we compared our data with that from a chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) generated by ENCODE (ENCODE Project Consortium, 2011) in the leukemia cell line K562. For this, we examined whether regions containing the GR-response eSNP bin and the corresponding probe gene overlap with physically interacting ChIA-PET tags (see Experimental Procedures). Twenty-five percent of the GR-response eSNP bin-probe gene combinations overlapped with chromatin interaction signals. This was significantly greater than 1,000 equally sized sets of randomly distributed GR-response eSNP bin, especially when restricting the analysis to more long-range eSNP bin-probe gene pairs with distances > 100 kb (fold enrichment>100kb = 1.57, permutation-based FDR>100kb = 0.007; see Experimental Procedures). To validate these long-range chromatin interactions, we used a chromatin conformation capture (3C) assay to confirm a physical interaction between the eSNP bin regions of the GR-response eSNP tag rs1379868 in the NRTN locus and the corresponding GR-stimulated transcript LONP1 (see Figures 4A and 4B), which is over 130 kb upstream. This eSNP bin includes a GR binding site and ChIA-PET tags (see Figure 4C), which interact with the transcription start site of the LONP1 gene. The 3C assay confirmed an increased chromatin interaction (p = 3.35 × 10−23, χ2 = 115.15 at baseline) of the eSNP bin with the TSS of the LONP1 gene (P4 in Figures 4C and 4D) in five LCLs. The average interaction frequency of these two sites was higher following stimulation with the GR-agonist dexamethasone (4.83 versus 5.65). These results suggest that long-range regulation of GR-response eQTLs could be mediated by direct chromatin interaction of enhancer regions with the respective transcription start sites.

Bottom Line: One putative biological mechanism implicates variability in the ability of cortisol, released in response to stress, to trigger a cascade of adaptive genomic and non-genomic processes through glucocorticoid receptor (GR) activation.Here, we demonstrate that common genetic variants in long-range enhancer elements modulate the immediate transcriptional response to GR activation in human blood cells.Moreover, these risk variants are associated with inappropriate amygdala reactivity, a transdiagnostic psychiatric endophenotype and an important stress hormone response trigger.

View Article: PubMed Central - PubMed

Affiliation: Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany.

Show MeSH
Related in: MedlinePlus