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Huang D, Shang W, Xu M, Wan Q, Zhang J, Tang X, Shen Y, Wang Y, Yu Y. Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension. Circ Res 2024; 135:e76-e93. [PMID: 38841840 DOI: 10.1161/circresaha.124.324455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Despite advances in understanding hypertension's genetic structure, how noncoding genetic variants influence it remains unclear. Studying their interaction with DNA methylation is crucial to deciphering this complex disease's genetic mechanisms. METHODS We investigated the genetic and epigenetic interplay in hypertension using whole-genome bisulfite sequencing. Methylation profiling in 918 males revealed allele-specific methylation and methylation quantitative trait loci. We engineered rs1275988T/C mutant mice using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), bred them for homozygosity, and subjected them to a high-salt diet. Telemetry captured their cardiovascular metrics. Protein-DNA interactions were elucidated using DNA pull-downs, mass spectrometry, and Western blots. A wire myograph assessed vascular function, and analysis of the Kcnk3 gene methylation highlighted the mutation's role in hypertension. RESULTS We discovered that DNA methylation-associated genetic effects, especially in non-cytosine-phosphate-guanine (non-CpG) island and noncoding distal regulatory regions, significantly contribute to hypertension predisposition. We identified distinct methylation quantitative trait locus patterns in the hypertensive population and observed that the onset of hypertension is influenced by the transmission of genetic effects through the demethylation process. By evidence-driven prioritization and in vivo experiments, we unearthed rs1275988 in a cell type-specific enhancer as a notable hypertension causal variant, intensifying hypertension through the modulation of local DNA methylation and consequential alterations in Kcnk3 gene expression and vascular remodeling. When exposed to a high-salt diet, mice with the rs1275988C/C genotype exhibited exacerbated hypertension and significant vascular remodeling, underscored by increased aortic wall thickness. The C allele of rs1275988 was associated with elevated DNA methylation levels, driving down the expression of the Kcnk3 gene by attenuating Nr2f2 (nuclear receptor subfamily 2 group F member 2) binding at the enhancer locus. CONCLUSIONS Our research reveals new insights into the complex interplay between genetic variations and DNA methylation in hypertension. We underscore hypomethylation's potential in hypertension onset and identify rs1275988 as a causal variant in vascular remodeling. This work advances our understanding of hypertension's molecular mechanisms and encourages personalized health care strategies.
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Affiliation(s)
- Dandan Huang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
- School of Food Science and Technology, Jiangnan University, Wuxi, China (D.H.)
| | - Wenlong Shang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Mengtong Xu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Qiangyou Wan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine (Q.W.)
| | - Jin Zhang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Xiaofeng Tang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Yujun Shen
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Yan Wang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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3
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Pettie KP, Mumbach M, Lea AJ, Ayroles J, Chang HY, Kasowski M, Fraser HB. Chromatin activity identifies differential gene regulation across human ancestries. Genome Biol 2024; 25:21. [PMID: 38225662 PMCID: PMC10789071 DOI: 10.1186/s13059-024-03165-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. RESULTS To address this, we devise an approach to search for lineage-specific selection on three critical steps in transcriptional regulation: chromatin activity, transcription factor binding, and chromosomal looping. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, we find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, we show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. CONCLUSIONS Overall, our study indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This work provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species.
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Affiliation(s)
- Kade P Pettie
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Maxwell Mumbach
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Julien Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Maya Kasowski
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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4
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Bhat S, Rotti H, Prasad K, Kabekkodu SP, Saadi AV, Shenoy SP, Joshi KS, Nesari TM, Shengule SA, Dedge AP, Gadgil MS, Dhumal VR, Salvi S, Satyamoorthy K. Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function. J Ayurveda Integr Med 2023; 14:100692. [PMID: 37018893 PMCID: PMC10122039 DOI: 10.1016/j.jaim.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 10/13/2022] [Accepted: 02/01/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The Indian traditional medicinal system, Ayurveda, describes several lifestyle practices, processes and medicines as an intervention to treat asthma. Rasayana therapy is one of them and although these treatment modules show improvement in bronchial asthma, their mechanism of action, particularly the effect on DNA methylation, is largely understudied. OBJECTIVES Our study aimed at identifying the contribution of DNA methylation changes in modulating bronchial asthma phenotype upon Ayurveda intervention. MATERIALS AND METHODS In this study, genome-wide methylation profiling in peripheral blood DNA of healthy controls and bronchial asthmatics before (BT) and after (AT) Ayurveda treatment was performed using array-based profiling of reference-independent methylation status (aPRIMES) coupled to microarray technique. RESULTS We identified 4820 treatment-associated DNA methylation signatures (TADS) and 11,643 asthma-associated DNA methylation signatures (AADS), differentially methylated [FDR (≤0.1) adjusted p-values] in AT and HC groups respectively, compared to BT group. Neurotrophin TRK receptor signaling pathway was significantly enriched for differentially methylated genes in bronchial asthmatics, compared to AT and HC subjects. Additionally, we identified over 100 differentially methylated immune-related genes located in the promoter/5'-UTR regions of TADS and AADS. Various immediate-early response and immune regulatory genes with functions such as transcription factor activity (FOXD1, FOXD2, GATA6, HOXA3, HOXA5, MZF1, NFATC1, NKX2-2, NKX2-3, RUNX1, KLF11), G-protein coupled receptor activity (CXCR4, PTGER4), G-protein coupled receptor binding (UCN), DNA binding (JARID2, EBF2, SOX9), SNARE binding (CAPN10), transmembrane signaling receptor activity (GP1BB), integrin binding (ITGA6), calcium ion binding (PCDHGA12), actin binding (TRPM7, PANX1, TPM1), receptor tyrosine kinase binding (PIK3R2), receptor activity (GDNF), histone methyltransferase activity (MLL5), and catalytic activity (TSTA3) were found to show consistent methylation status between AT and HC group in microarray data. CONCLUSIONS Our study reports the DNA methylation-regulated genes in bronchial asthmatics showing improvement in symptoms after Ayurveda intervention. DNA methylation regulation in the identified genes and pathways represents the Ayurveda intervention responsive genes and may be further explored as diagnostic, prognostic, and therapeutic biomarkers for bronchial asthma in peripheral blood.
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Affiliation(s)
- Smitha Bhat
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Harish Rotti
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keshava Prasad
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushma P Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kalpana S Joshi
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Tanuja M Nesari
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sushant A Shengule
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Amrish P Dedge
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Maithili S Gadgil
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Vikram R Dhumal
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sundeep Salvi
- Department of Pulmonary Medicine, Chest Research Foundation, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Yan B, Wang D, Vaisvila R, Sun Z, Ettwiller L. Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment. Genome Res 2022; 32:2079-2091. [PMID: 36332968 PMCID: PMC9808626 DOI: 10.1101/gr.277080.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Covalent modifications of genomic DNA are crucial for most organisms to survive. Amplicon-based high-throughput sequencing technologies erase all DNA modifications to retain only sequence information for the four canonical nucleobases, necessitating specialized technologies for ascertaining epigenetic information. To also capture base modification information, we developed Methyl-SNP-seq, a technology that takes advantage of the complementarity of the double helix to extract the methylation and original sequence information from a single DNA molecule. More specifically, Methyl-SNP-seq uses bisulfite conversion of one of the strands to identify cytosine methylation while retaining the original four-bases sequence information on the other strand. As both strands are locked together to link the dual readouts on a single paired-end read, Methyl-SNP-seq allows detecting the methylation status of any DNA even without a reference genome. Because one of the strands retains the original four nucleotide composition, Methyl-SNP-seq can also be used in conjunction with standard sequence-specific probes for targeted enrichment and amplification. We show the usefulness of this technology in a broad spectrum of applications ranging from allele-specific methylation analysis in humans to identification of methyltransferase specificity in complex bacterial communities.
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Affiliation(s)
- Bo Yan
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Duan Wang
- SLC Management, Wellesley Hills, Massachusetts 02481, USA
| | | | - Zhiyi Sun
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
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Zhang Y, Liu C. Evaluating the challenges and reproducibility of studies investigating DNA methylation signatures of psychological stress. Epigenomics 2022; 14:405-421. [PMID: 35170363 PMCID: PMC8978984 DOI: 10.2217/epi-2021-0190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
Abstract
Psychological stress can increase the risk of a wide range of negative health outcomes. Studies have been completed to determine if DNA methylation changes occur in the human brain because of stress and are associated with long-term effects and disease, but results have been inconsistent. Human candidate gene studies (150) and epigenome-wide association studies (67) were systematically evaluated to assess how DNA methylation is impacted by stress during the prenatal period, early childhood and adulthood. The association between DNA methylation of NR3C1 exon 1F and child maltreatment and early life adversity was well demonstrated, but other genes did not exhibit a clear association. The reproducibility of individual CpG sites in epigenome-wide association studies was also poor. However, biological pathways, including stress response, brain development and immunity, have been consistently identified across different stressors throughout the life span. Future studies would benefit from the increased sample size, longitudinal design, standardized methodology, optimal quality control, and improved statistical procedures.
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Affiliation(s)
- Yun Zhang
- Medical Department, Northwest Minzu University, Lanzhou, Gansu, 730000, China
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, Gansu, 730000, China
| | - Chunyu Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410078, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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7
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Reid BM, Fridley BL. DNA Methylation in Ovarian Cancer Susceptibility. Cancers (Basel) 2020; 13:E108. [PMID: 33396385 PMCID: PMC7795210 DOI: 10.3390/cancers13010108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations are somatically acquired over the lifetime and during neoplastic transformation but may also be inherited as widespread 'constitutional' alterations in normal tissues that can cause cancer predisposition. Epithelial ovarian cancer (EOC) has an established genetic susceptibility and mounting epidemiological evidence demonstrates that DNA methylation (DNAm) intermediates as well as independently contributes to risk. Targeted studies of known EOC susceptibility genes (CSGs) indicate rare, constitutional BRCA1 promoter methylation increases familial and sporadic EOC risk. Blood-based epigenome-wide association studies (EWAS) for EOC have detected a total of 2846 differentially methylated probes (DMPs) with 71 genes replicated across studies despite significant heterogeneity. While EWAS detect both symptomatic and etiologic DMPs, adjustments and analytic techniques may enrich risk associations, as evidenced by the detection of dysregulated methylation of BNC2-a known CSG identified by genome-wide associations studies (GWAS). Integrative genetic-epigenetic approaches have mapped methylation quantitative trait loci (meQTL) to EOC risk, revealing DNAm variations that are associated with nine GWAS loci and, further, one novel risk locus. Increasing efforts to mapping epigenome variation across populations and cell types will be key to decoding both the genomic and epigenomic causal pathways to EOC.
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Affiliation(s)
- Brett M. Reid
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Brooke L. Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
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Zhao Q, Dacre M, Nguyen T, Pjanic M, Liu B, Iyer D, Cheng P, Wirka R, Kim JB, Fraser HB, Quertermous T. Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping. Genome Biol 2020; 21:135. [PMID: 32513244 PMCID: PMC7278146 DOI: 10.1186/s13059-020-02049-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells (HCASMCs). RESULTS We use a pooling approach with HCASMC lines to map regulatory variants that mediate binding of the CAD-associated transcription factor TCF21 with ChIPseq studies (bQTLs), variants that regulate chromatin accessibility with ATACseq studies (caQTLs), and chromosomal looping with Hi-C methods (clQTLs). We examine the overlap of these QTLs and their relationship to smooth muscle-specific genes and transcription factors. Further, we use multiple analyses to show that these QTLs are highly associated with CAD GWAS loci and correlate to lead SNPs where they show allelic effects. By utilizing genome editing, we verify that identified functional variants can regulate both chromatin accessibility and chromosomal looping, providing new insights into functional mechanisms regulating chromatin state and chromosomal structure. Finally, we directly link the disease-associated TGFB1-SMAD3 pathway to the CAD-associated FN1 gene through a response QTL that modulates both chromatin accessibility and chromosomal looping. CONCLUSIONS Together, these studies represent the most thorough mapping of multiple QTL types in a highly disease-relevant primary cultured cell type and provide novel insights into their functional overlap and mechanisms that underlie these genomic features and their relationship to disease risk.
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Affiliation(s)
- Quanyi Zhao
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Michael Dacre
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Trieu Nguyen
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Milos Pjanic
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Boxiang Liu
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Dharini Iyer
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Paul Cheng
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Robert Wirka
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Juyong Brian Kim
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Dr. Falk CVRC, Stanford, CA, 94305, USA.
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9
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Fan Y, Vilgalys TP, Sun S, Peng Q, Tung J, Zhou X. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Genome Biol 2019; 20:220. [PMID: 31651351 PMCID: PMC6813132 DOI: 10.1186/s13059-019-1813-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
Identifying genetic variants that are associated with methylation variation-an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping-is important for understanding the epigenetic mechanisms underlying genotype-trait associations. Here, we develop a statistical method, IMAGE, for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. We compare IMAGE with existing approaches through extensive simulation. We also apply IMAGE to analyze two bisulfite sequencing studies, in which IMAGE identifies more mQTL than existing approaches.
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Affiliation(s)
- Yue Fan
- Systems Engineering Institute, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tauras P Vilgalys
- Departments of Evolutionary Anthropology and Biology, Duke University, Durham, NC, 27708, USA
| | - Shiquan Sun
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Qinke Peng
- Systems Engineering Institute, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Jenny Tung
- Departments of Evolutionary Anthropology and Biology, Duke University, Durham, NC, 27708, USA
- Duke University Population Research Institute, Duke University, Durham, NC, 27708, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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10
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Tehranchi A, Hie B, Dacre M, Kaplow I, Pettie K, Combs P, Fraser HB. Fine-mapping cis-regulatory variants in diverse human populations. eLife 2019; 8:39595. [PMID: 30650056 PMCID: PMC6335058 DOI: 10.7554/elife.39595] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/30/2018] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWAS) are a powerful approach for connecting genotype to phenotype. Most GWAS hits are located in cis-regulatory regions, but the underlying causal variants and their molecular mechanisms remain unknown. To better understand human cis-regulatory variation, we mapped quantitative trait loci for chromatin accessibility (caQTLs)—a key step in cis-regulation—in 1000 individuals from 10 diverse populations. Most caQTLs were shared across populations, allowing us to leverage the genetic diversity to fine-map candidate causal regulatory variants, several thousand of which have been previously implicated in GWAS. In addition, many caQTLs that affect the expression of distal genes also alter the landscape of long-range chromosomal interactions, suggesting a mechanism for long-range expression QTLs. In sum, our results show that molecular QTL mapping integrated across diverse populations provides a high-resolution view of how worldwide human genetic variation affects chromatin accessibility, gene expression, and phenotype. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that minor issues remain unresolved (see decision letter).
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Affiliation(s)
- Ashley Tehranchi
- Department of Biology, Stanford University, Stanford, United States
| | - Brian Hie
- Department of Computer Science, Stanford University, Stanford, United States
| | - Michael Dacre
- Department of Biology, Stanford University, Stanford, United States
| | - Irene Kaplow
- Department of Computer Science, Stanford University, Stanford, United States
| | - Kade Pettie
- Department of Biology, Stanford University, Stanford, United States
| | - Peter Combs
- Department of Biology, Stanford University, Stanford, United States
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, United States
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11
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Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Res 2018; 28:1364-1371. [PMID: 30093547 PMCID: PMC6120621 DOI: 10.1101/gr.232587.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%-2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with transposase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression. Using these transposase-accessible loci to represent the cis-regulatory loci in the genome, we compared the representation of these loci between WGBS and other genome-wide DNA methylation assays, showing WGBS to outperform substantially all of the alternatives. We conclude that it is now technologically and financially feasible to perform WGBS in larger numbers of samples with greater accuracy than previously possible.
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Affiliation(s)
- Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Will Liao
- New York Genome Center, New York, New York 10013, USA
| | - Frank Wos
- New York Genome Center, New York, New York 10013, USA
| | - Andrew D Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | - Toby Bloom
- New York Genome Center, New York, New York 10013, USA
| | | | - Soren Germer
- New York Genome Center, New York, New York 10013, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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12
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Gallagher MD, Chen-Plotkin AS. The Post-GWAS Era: From Association to Function. Am J Hum Genet 2018; 102:717-730. [PMID: 29727686 DOI: 10.1016/j.ajhg.2018.04.002] [Citation(s) in RCA: 479] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
During the past 12 years, genome-wide association studies (GWASs) have uncovered thousands of genetic variants that influence risk for complex human traits and diseases. Yet functional studies aimed at delineating the causal genetic variants and biological mechanisms underlying the observed statistical associations with disease risk have lagged. In this review, we highlight key advances in the field of functional genomics that may facilitate the derivation of biological meaning post-GWAS. We highlight the evidence suggesting that causal variants underlying disease risk often function through regulatory effects on the expression of target genes and that these expression effects might be modest and cell-type specific. We moreover discuss specific studies as proof-of-principle examples for current statistical, bioinformatic, and empirical bench-based approaches to downstream elucidation of GWAS-identified disease risk loci.
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13
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Dougherty L, Singh R, Brown S, Dardick C, Xu K. Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1499-1516. [PMID: 29361034 PMCID: PMC5888915 DOI: 10.1093/jxb/erx490] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/19/2017] [Indexed: 05/19/2023]
Abstract
To unlock the power of next generation sequencing-based bulked segregant analysis in allele discovery in out-crossing woody species, and to understand the genetic control of the weeping trait, an F1 population from the cross 'Cheal's Weeping' × 'Evereste' was used to create two genomic DNA pools 'weeping' (17 progeny) and 'standard' (16 progeny). Illumina pair-end (2 × 151 bp) sequencing of the pools to a 27.1× (weeping) and a 30.4× (standard) genome (742.3 Mb) coverage allowed detection of 84562 DNA variants specific to 'weeping', 92148 specific to 'standard', and 173169 common to both pools. A detailed analysis of the DNA variant genotypes in the pools predicted three informative segregation types of variants: (type I) in weeping pool-specific variants, and (type II) and (type III) in variants common to both pools, where the first allele is assumed to be weeping linked and the allele shown in bold is a variant in relation to the reference genome. Conducting variant allele frequency and density-based mappings revealed four genomic regions with a significant association with weeping: a major locus, Weeping (W), on chromosome 13 and others on chromosomes 10 (W2), 16 (W3), and 5 (W4). The results from type I variants were noisier and less certain than those from type II and type III variants, demonstrating that although type I variants are often the first choice, type II and type III variants represent an important source of DNA variants that can be exploited for genetic mapping in out-crossing woody species. Confirmation of the mapping of W and W2, investigation into their genetic interactions, and identification of expressed genes in the W and W2 regions provided insight into the genetic control of weeping and its expressivity in Malus.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | - Raksha Singh
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | | | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
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14
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Zeng Q, Chen X, Ning C, Zhu Q, Yao Y, Zhao Y, Luan F. Methylation of the genes ROD1, NLRC5, and HKR1 is associated with aging in Hainan centenarians. BMC Med Genomics 2018; 11:7. [PMID: 29394898 PMCID: PMC5797414 DOI: 10.1186/s12920-018-0334-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/25/2018] [Indexed: 12/18/2022] Open
Abstract
Background Human aging is a hot topic in biology, and it has been associated with DNA methylation changes at specific genomic sites. We aimed to study the changes of DNA methylation at a single-CpG-site resolution using peripheral blood samples from centenarians. Methods Using Illumina 450 K Methylation BeadChip microarray assays, we carried out a pool-based, epigenome-wide investigation of DNA methylation of blood samples from 12 centenarians and 12 healthy controls. Differentially methylated cytosine-phosphate-guanosine (CpG) sites were selected for further pyrosequencing analysis of blood samples from 30 centenarians and 30 healthy controls. Result We identified a total of 31 high-confidence CpG sites with differential methylation profiles between the groups: 9 (29%) were hypermethylated and 22 (71%) were hypomethylated in centenarians. It was also found that hypermethylation of HKR1 and hypomethylation of ROD1 and NLRC5 genes strongly correlated with age in centenarians. Conclusion Our results indicate that the methylation profile combination of HKR1, ROD1, and NLRC5 could be a promising biomarker for aging in Hainan centenarians. Electronic supplementary material The online version of this article (10.1186/s12920-018-0334-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qian Zeng
- Hainan branch of PLA General Hospital, Sanya, 572000, China
| | - Xiaoping Chen
- Hainan branch of PLA General Hospital, Sanya, 572000, China
| | - Chaoxue Ning
- Hainan branch of PLA General Hospital, Sanya, 572000, China
| | - Qiao Zhu
- Hainan branch of PLA General Hospital, Sanya, 572000, China
| | - Yao Yao
- Hainan branch of PLA General Hospital, Sanya, 572000, China
| | - Yali Zhao
- Hainan branch of PLA General Hospital, Sanya, 572000, China.
| | - Fuxin Luan
- Hainan branch of PLA General Hospital, Sanya, 572000, China.
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15
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Kader F, Ghai M, Maharaj L. The effects of DNA methylation on human psychology. Behav Brain Res 2017; 346:47-65. [PMID: 29237550 DOI: 10.1016/j.bbr.2017.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Leah Maharaj
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
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16
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Zeng H, Gifford DK. Predicting the impact of non-coding variants on DNA methylation. Nucleic Acids Res 2017; 45:e99. [PMID: 28334830 PMCID: PMC5499808 DOI: 10.1093/nar/gkx177] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/13/2017] [Indexed: 12/22/2022] Open
Abstract
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation. CpGenie produces allele-specific DNA methylation prediction with single-nucleotide sensitivity that enables accurate prediction of methylation quantitative trait loci (meQTL). We demonstrate that CpGenie prioritizes validated GWAS SNPs, and contributes to the prediction of functional non-coding variants, including expression quantitative trait loci (eQTL) and disease-associated mutations. CpGenie is publicly available to assist in identifying and interpreting regulatory non-coding variants.
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Affiliation(s)
- Haoyang Zeng
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology Cambridge, MA 02142, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology Cambridge, MA 02142, USA
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17
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Schröder C, Leitão E, Wallner S, Schmitz G, Klein-Hitpass L, Sinha A, Jöckel KH, Heilmann-Heimbach S, Hoffmann P, Nöthen MM, Steffens M, Ebert P, Rahmann S, Horsthemke B. Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function. Epigenetics Chromatin 2017; 10:37. [PMID: 28747224 PMCID: PMC5530492 DOI: 10.1186/s13072-017-0144-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/20/2017] [Indexed: 01/23/2023] Open
Abstract
Background There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. Results We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before. The DMRs fall into different chromatin states, where methylation is inversely correlated with active, but not repressive histone marks. However, methylation is not correlated with the expression of associated genes. High-resolution single nucleotide polymorphism (SNP) genotyping of the five donors revealed evidence for a role of cis-acting genetic variation in establishing methylation patterns. To validate this finding in a larger cohort, we performed genome-wide association studies (GWAS) using SNP genotypes and 450k array methylation data from blood samples of 1128 individuals. Only 30/157 (19%) DMRs include at least one 450k CpG, which shows that these arrays miss a large proportion of DNA methylation variation. In most cases, the GWAS peak overlapped the CpG position, and these regions are enriched for CREB group, NF-1, Sp100 and CTCF binding motifs. In two cases, there was tentative evidence for a trans-effect by KRAB zinc finger proteins. Conclusions Allele-specific DNA methylation occurs in discrete chromosomal regions and is driven by genetic variation in cis and trans, but in general has little effect on gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0144-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher Schröder
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Stefan Wallner
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology, Kiel University, University Hospital, Kiel, Germany
| | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - Peter Ebert
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany.
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18
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Angermueller C, Lee HJ, Reik W, Stegle O. DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning. Genome Biol 2017; 18:67. [PMID: 28395661 PMCID: PMC5387360 DOI: 10.1186/s13059-017-1189-z] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/07/2017] [Indexed: 12/31/2022] Open
Abstract
Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methylation states are critical to enable genome-wide analyses. We report DeepCpG, a computational approach based on deep neural networks to predict methylation states in single cells. We evaluate DeepCpG on single-cell methylation data from five cell types generated using alternative sequencing protocols. DeepCpG yields substantially more accurate predictions than previous methods. Additionally, we show that the model parameters can be interpreted, thereby providing insights into how sequence composition affects methylation variability.
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Affiliation(s)
- Christof Angermueller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Heather J Lee
- Epigenetics Programme, Babraham Institute, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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19
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Barozzi I, Visel A, Dickel DE. Fishing for Function in the Human Gene Pool. Trends Genet 2016; 32:392-394. [PMID: 27220646 DOI: 10.1016/j.tig.2016.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 11/28/2022]
Abstract
Identification and characterization of causal non-coding variants in human genomes is challenging and requires substantial experimental resources. A new study by Tehranchi et al. describes a cost-effective approach for accurate mapping of molecular quantitative trait loci (QTLs) from pooled samples, a powerful way to link disease-associated changes to molecular functions.
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Affiliation(s)
- Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, California, USA.
| | - Diane E Dickel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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20
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Tehranchi AK, Myrthil M, Martin T, Hie BL, Golan D, Fraser HB. Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk. Cell 2016; 165:730-41. [PMID: 27087447 DOI: 10.1016/j.cell.2016.03.041] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/30/2015] [Accepted: 03/23/2016] [Indexed: 01/08/2023]
Abstract
Cis-regulatory elements such as transcription factor (TF) binding sites can be identified genome-wide, but it remains far more challenging to pinpoint genetic variants affecting TF binding. Here, we introduce a pooling-based approach to mapping quantitative trait loci (QTLs) for molecular-level traits. Applying this to five TFs and a histone modification, we mapped thousands of cis-acting QTLs, with over 25-fold lower cost compared to standard QTL mapping. We found that single genetic variants frequently affect binding of multiple TFs, and CTCF can recruit all five TFs to its binding sites. These QTLs often affect local chromatin and transcription but can also influence long-range chromosomal contacts, demonstrating a role for natural genetic variation in chromosomal architecture. Thousands of these QTLs have been implicated in genome-wide association studies, providing candidate molecular mechanisms for many disease risk loci and suggesting that TF binding variation may underlie a large fraction of human phenotypic variation.
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Affiliation(s)
| | - Marsha Myrthil
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Trevor Martin
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Brian L Hie
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - David Golan
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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21
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Gaunt TR, Shihab HA, Hemani G, Min JL, Woodward G, Lyttleton O, Zheng J, Duggirala A, McArdle WL, Ho K, Ring SM, Evans DM, Davey Smith G, Relton CL. Systematic identification of genetic influences on methylation across the human life course. Genome Biol 2016; 17:61. [PMID: 27036880 PMCID: PMC4818469 DOI: 10.1186/s13059-016-0926-z] [Citation(s) in RCA: 387] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/15/2016] [Indexed: 12/13/2022] Open
Abstract
Background The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci (mQTL)) at five different life stages in human blood: children at birth, childhood, adolescence and their mothers during pregnancy and middle age. Results We show that genetic effects on methylation are highly stable across the life course and that developmental change in the genetic contribution to variation in methylation occurs primarily through increases in environmental or stochastic effects. Though we map a large proportion of the cis-acting genetic variation, a much larger component of genetic effects influencing methylation are acting in trans. However, only 7 % of discovered mQTL are trans-effects, suggesting that the trans component is highly polygenic. Finally, we estimate the contribution of mQTL to variation in complex traits and infer that methylation may have a causal role consistent with an infinitesimal model in which many methylation sites each have a small influence, amounting to a large overall contribution. Conclusions DNA methylation contains a significant heritable component that remains consistent across the lifespan. Our results suggest that the genetic component of methylation may have a causal role in complex traits. The database of mQTL presented here provide a rich resource for those interested in investigating the role of methylation in disease. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0926-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Geoff Woodward
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Oliver Lyttleton
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Aparna Duggirala
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Wendy L McArdle
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Karen Ho
- Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Avon Longitudinal Study of Parents and Children (ALSPAC) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - David M Evans
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit (IEU) & School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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22
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Legendre C, Gooden GC, Johnson K, Martinez RA, Liang WS, Salhia B. Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer. Clin Epigenetics 2015; 7:100. [PMID: 26380585 PMCID: PMC4573288 DOI: 10.1186/s13148-015-0135-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/08/2015] [Indexed: 01/28/2023] Open
Abstract
Background A number of clinico-pathological criteria and molecular profiles have been used to stratify patients into high- and low-risk groups. Currently, there are still no effective methods to determine which patients harbor micrometastatic disease after standard breast cancer therapy and who will eventually develop local or distant recurrence. The purpose of our study was to identify circulating DNA methylation changes that can be used for prediction of metastatic breast cancer (MBC). Results Differential methylation analysis revealed ~5.0 × 106 differentially methylated CpG loci in MBC compared with healthy individuals (H) or disease-free survivors (DFS). In contrast, there was a strong degree of similarity between H and DFS. Overall, MBC demonstrated global hypomethylation and focal CpG island (CPGI) hypermethylation. Data analysis identified 21 novel hotspots, within CpG islands, that differed most dramatically in MBC compared with H or DFS. Conclusions This unbiased analysis of cell-free (cf) DNA identified 21 DNA hypermethylation hotspots associated with MBC and demonstrated the ability to distinguish tumor-specific changes from normal-derived signals at the whole-genome level. This signature is a potential blood-based biomarker that could be advantageous at the time of surgery and/or after the completion of chemotherapy to indicate patients with micrometastatic disease who are at a high risk of recurrence and who could benefit from additional therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0135-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christophe Legendre
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ USA
| | - Gerald C Gooden
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ USA
| | - Kyle Johnson
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ USA
| | - Rae Anne Martinez
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ USA
| | - Winnie S Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ USA
| | - Bodour Salhia
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ USA
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