DNA methylation represents an important layer of epigenetic regulation on the activity of the human genome. It is well known that there is a tremendous amount of genetic variation among human individuals and populations. Such genetic variation leads to the variation of gene expression among different individuals for the same cell types or tissues. Accumulating evidence suggests that the epigenome, including methylome, also varies from one individual to another. Such variation is believed to play functional roles in the individual variation of a variety of phenotypes, including many human diseases. Yet the detailed mechanisms and the extent to which the epigenome is individualized by the ensemble of genetic polymorphisms remains barely investigated. We will comprehensively characterize the effects of genetic polymorphisms on the individual human methylomes. The ultimate goal of this study is to understand how DNA methylation is organized along single human chromosomes, how do such local or long-range organizations relate to the functions, and how do genetic variations affect the functional organization of DNA methylation.
The specific aims are: (1) Experimentally construction of fully phased diploid human genomes, which will serve as a chassis to connect short and long range cis-regulators of DNA methylation, and to link methylation to the binding of protein cis-regulators as well as gene expression. (2) Mapping cis-regulatory variants for DNA methylation by integrating mQTL associative mapping with allele-specific methylation analysis. This proposed study will produce a method for constructing phased diploid methylome and an analytic framework for studying long-range genetic regulation of the DNA methylome. We will identify a list of cis-regulatory variants in the HapMap samples used in this study. The experimental and analytical framework will be applicable to the study of the genetic effects on a variety of other epigenetic modifications.

Public Health Relevance

Epigenetic processes modulate the packaging and function of the human genome in normal developmental processes and in many pathologic states, including human cancers and other common diseases. Disease susceptibility is modulated by both genetic and environmental factors through epigenetic changes. Investigating the effects of genetic variants on and DNA methylome will help elucidating the relative contributions of gene and environment to human diseases, and enabling the identification of more accurate biomarkers for disease prognosis and diagnosis.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Krasnewich, Donna M
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University of California San Diego
Engineering (All Types)
Schools of Arts and Sciences
La Jolla
United States
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Diep, Dinh; Plongthongkum, Nongluk; Zhang, Kun (2018) Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes. Methods Mol Biol 1708:365-382
Guo, Shicheng; Diep, Dinh; Plongthongkum, Nongluk et al. (2017) Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat Genet 49:635-642
BLUEPRINT consortium (2016) Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 34:726-37
Sos, Brandon Chin; Fung, Ho-Lim; Gao, Derek Rui et al. (2016) Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biol 17:20
Gu, Ying; Liu, Guang-Hui; Plongthongkum, Nongluk et al. (2014) Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell 5:59-68
Plongthongkum, Nongluk; Diep, Dinh H; Zhang, Kun (2014) Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet 15:647-61
Plongthongkum, Nongluk; van Eijk, Kristel R; de Jong, Simone et al. (2014) Characterization of genome-methylome interactions in 22 nuclear pedigrees. PLoS One 9:e99313
Lo, Christine; Liu, Rui; Lee, Jehyuk et al. (2013) On the design of clone-based haplotyping. Genome Biol 14:R100
Gole, Jeff; Gore, Athurva; Richards, Andrew et al. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol 31:1126-32
Lee, Ho Suk; Chu, Wai Keung; Zhang, Kun et al. (2013) Microfluidic devices with permeable polymer barriers for capture and transport of biomolecules and cells. Lab Chip 13:3389-97

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