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Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells

ABSTRACT: Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells

PROVIDER: PRJNA698386 | ENA |

REPOSITORIES: ENA

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Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [WGBS]

Project description:Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [WGBS]

| PRJNA699444 | ENA

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [WGBS]

Project description:Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. Nearly a quarter of autosomal regions bear potentially differential chromatin modifications, with promoters/CpG islands for H3K27me3/H2AK119ub1 and evolutionarily young retrotransposons for H3K4me3. We identify 145 large autosomal blocks (≥100 kb) with differential H3K9me3 enrichment, many of which are lamina-associated domains (LADs) in somatic, but not in embryonic stem cells. A majority of these epigenomic heterogeneities are independent of genetic variations. We identify an X-chromosome state with chromosome-wide H3K9me3 that stably prevents X-chromosome erosion. Importantly, the germline potential of female hiPSCs correlates with X-chromosome inactivation. We propose that inherent genomic properties, including CpG density, transposons, and LADs, engender epigenomic heterogeneity in hiPSCs.

2021-11-03 | GSE166138 | GEO

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [RNA-seq]

Project description:Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [RNA-seq]

| PRJNA698387 | ENA

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [ChIP-seq]

Project description:Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [ChIP-seq]

| PRJNA698388 | ENA

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [RNA-seq]

2021-11-03 | GSE165868 | GEO

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [ChIP-seq]

2021-11-03 | GSE165867 | GEO

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-11-03 | GSE165869 | GEO

Single-cell epigenomic variability reveals functional cancer heterogeneity

Project description:Background: Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity, but is difficult to detect and assess functionally. Results: We develop a strategy to bridge the gap between measurement and function in single-cell epigenomics. Using single-cell chromatin accessibility and RNA-seq data in K562 leukemic cells, we identify the cell surface marker CD24 as co-varying with chromatin accessibility changes linked to GATA transcription factors in single cells. Fluorescence-activated cell sorting of CD24 high vs. low cells prospectively isolated GATA1 and GATA2 high vs. low cells. GATA high vs. low cells express differential gene regulatory networks, differential sensitivity to the drug imatinib mesylate, and differential self-renewal capacity. Lineage tracing experiments show that GATA/CD24hi cells have the capability to rapidly reconstitute the heterogeneity within the entire starting population, suggesting that GATA expression levels drive a phenotypically relevant source of epigenomic plasticity. Conclusion: Single-cell chromatin accessibility can guide prospective characterization of cancer heterogeneity. Epigenomic subpopulations in cancer impact drug sensitivity and the clonal dynamics of cancer evolution.

2016-12-12 | GSE76224 | GEO

Differences in cell cycle status underlie transcriptional heterogeneity in the HSC compartment

Project description:Differences in cell cycle status underlie transcriptional heterogeneity in the HSC compartment

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Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity

Project description:Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity

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