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Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells

ABSTRACT: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression. It is a mystery how chromatin marks in regulatory elements are modulated to establish cell type-specific gene expression. Here we profiled a variety of epigenetic marks in the regulatory elements using massive ChIP-seq (n=84). We uncovered two classes of regulatory elements: Class I was identified with ubiquitous enhancer (H3K4me1) and promoter (H3K4me3) marks in all cell types, whereas Class II was enriched with H3K4me1 and H3K4me3 in a cell type-specific manner. For common genes regulated by both promoters and enhancers, Class I promoters displayed dominant regulatory effects on transcriptional abundance. Moreover, human iPSCs and somatic cells selected their preferential regulatory elements to maintain cell type-specific gene expression. Our study provides valuable resources for deciphering the epigenetic modulation of regulatory elements that fine-tune spatiotemporal gene expression in human development and diseases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97033 | GEO | 2017/12/04

SECONDARY ACCESSION(S): PRJNA380431

REPOSITORIES: GEO

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Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells

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