The Genotype-Tissue Expression project (GTEx) is expanding the availability of primary tissue samples for studying the impact of genetic variation on gene expression across individuals and tissues. However, inter-individual variation in gene expression level can often result from the combined effects of multiple variants, each of which may affect the activity of different regulatory regions in complex ways, and also integrate complex post-transcriptional events. Thus, to directly assess the effect of sequence variants on regulatory elements, we propose to systematic profile epigenetic modifications on stored GTEx biospecimens to enhance the analysis of gene expression variation already available and planned by the GTEx consortium.
Aim 1. We will use whole-genome bisulfite sequencing (WGBS) to profile DNA methylation levels for all 28M CpGs in the genome of 20 individuals in 8 GTEx tissues. We will use these to identify variable methylated regions (VMRs) across cell types and across individuals, to evaluate the effects of eQTL SNPs on DNA methylation levels of neighboring CpGs, and to recognize allele-specific methylation (ASM) regions and their tissue specificity.
Aim 2. We will systematically profile DNA methylation levels across 250 individuals in the same 8 tissues using hybrid-selection bisulfite sequencing (HSBS) for a subset of 2M regions selected within enhancer-associated, eQTL-associated, and inter-individual variable regions. We will use these to predict methylation quantitative trait loci (meQTLs) in each tissue, relate these to GTEx expression QTLs (eQTLs) for the same tissues to provide mechanistic hypotheses for inter- individual gene expression variation, and to discover meQTLs for genes where no single eQTL is significant.
Aim 3. We will use chromatin immunoprecipitation sequencing (ChIP-Seq) to profile enhancer- and promoter-associated histone modification H3K27ac in 6 GTEx brain samples across 100 individuals, to recognize genotype-associated enhancer regions and enhQTLs. We will relate these to eQTLs in the same tissues and meQTLs discovered using HSBS on enhancer-proximal and eQTL proximal CpGs to generate mechanistic models for regulatory changes associated with genotype variation. We will work closely with the GTEx Analysis Consortium to integrate GTEx eQTLs with our predicted meQTLs, ASM regions, and enhQTLs to relate regulatory region variation to gene expression variation and to genome-wide association studies to understand the role of sequence variation in tissue-specific gene regulation, gene expression, and human disease.

Public Health Relevance

Most human variants associated with disease are non-coding and largely uncharacterized, making it a great priority to understand the cell types in which they act and their mechanism of action. To address this challenge, we propose to characterize the regulatory impact of genetic variation in eight human tissues and six brain regions with important roles in diabetes, heart disease, cancer, and neuropsychiatric disease. We construct epigenomic maps of active and repressed regulatory elements across 250 individuals in each tissue and 100 individuals in brain regions, and integrate these with genetic variation and gene expression variation as part of the Genotype-Tissue Expression (GTEx) project, providing a powerful resource for deciphering the basic biology of gene regulation in diverse tissues and the mechanistic molecular basis of human disease.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project--Cooperative Agreements (U01)
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Special Emphasis Panel (ZRG1-IMST-M (50))
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Volpi, Simona
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Massachusetts Institute of Technology
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Onuchic, Vitor; Lurie, Eugene; Carrero, Ivenise et al. (2018) Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science 361:
Wang, Yang; Li, Yue; Yue, Minghui et al. (2018) N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nat Neurosci 21:195-206
Gamazon, Eric R; Segrè, Ayellet V; van de Bunt, Martijn et al. (2018) Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nat Genet 50:956-967
Tukiainen, Taru; Villani, Alexandra-Chloé; Yen, Angela et al. (2017) Landscape of X chromosome inactivation across human tissues. Nature 550:244-248
eGTEx Project (2017) Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nat Genet 49:1664-1670
Li, Xin; Kim, Yungil; Tsang, Emily K et al. (2017) The impact of rare variation on gene expression across tissues. Nature 550:239-243
Saha, Ashis; Kim, Yungil; Gewirtz, Ariel D H et al. (2017) Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res 27:1843-1858
Liu, Yaping; Sarkar, Abhishek; Kheradpour, Pouya et al. (2017) Evidence of reduced recombination rate in human regulatory domains. Genome Biol 18:193
Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran et al. (2017) Dynamic landscape and regulation of RNA editing in mammals. Nature 550:249-254
Yang, Fan; Wang, Jiebiao; GTEx Consortium et al. (2017) Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res 27:1859-1871

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