The epigenome is the ensemble of chemical modifications of DNA and chromatin that modulates genomic activities such as the transcription of messenger RNA, which further serves as the template of protein syntheses. The epigenome plays instrumental roles in gene regulation during human development and in healthy as well as disease conditions. Although the genome is nearly identical in each cell in the human body, epigenomes are highly dynamic across tissues and between cell types composing the tissues/organs. The current knowledge of the epigenome is largely built on analyses of human tissues without distinguishing the potential distinct epigenomes of individual cells. The heterogeneity of certain biological processes, such as the reprogramming of somatic cells to the highly medically valuable induced pluripotent stem cells (iPSCs), also requires the capability of analyzing the epigenome and transcriptome of single cells. A powerful approach for studying epigenomic regulation is to profile multiple components of the epigenome (e.g. DNA methylation or histone modifications) and the transcriptome from the same sample. Such multi-dimensional analysis of single cells is highly challenging since most current methods are uni-dimensional. High-throughput sequencing based methods will be developed by the project to analyze multiple epigenomic components, including the DNA methylome and chromatin accessibility, and the transcriptome of single human cells. These methods will be first developed using cultured human cells and later adapted to primary human tissues. As a model for assay development, the methods will be applied to study single cell epigenomic diversity during the somatic cell reprogramming process that generates iPSCs. If successfully developed, these methods will greatly facilitate epigenomic studies of diverse cell types in complex human tissues and in heterogeneous diseases such as cancer.

Public Health Relevance

The epigenome includes all of the chemical modifications to DNA and chromatin that modulated gene activity through controlling the accessibility to the genome. Human tissues, organs and cell types are associated with highly distinct epigenomic patterns. The proposed methods will allow the generation of multi-dimensional epigenomic and transcriptomic maps from single human cells, which will enable more specific epigenomic analyses of normal human development as well as heterogeneous diseases such as cancer at a single cell level.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Exploratory/Developmental Grants (R21)
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Special Emphasis Panel (ZRG1)
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Smith, Michael
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Salk Institute for Biological Studies
La Jolla
United States
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Luo, Chongyuan; Rivkin, Angeline; Zhou, Jingtian et al. (2018) Robust single-cell DNA methylome profiling with snmC-seq2. Nat Commun 9:3824
Luo, Chongyuan; Hajkova, Petra; Ecker, Joseph R (2018) Dynamic DNA methylation: In the right place at the right time. Science 361:1336-1340
Luo, Chongyuan; Keown, Christopher L; Kurihara, Laurie et al. (2017) Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science 357:600-604