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Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [Affymetrix]

ABSTRACT: Memory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human naïve and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to naïve cells, revealing specific genes more rapidly expressed in memory compared to naïve cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression. transcriptome of primary human naïve and memory CD4 T cells at rest and 48 hours post-activation.

ORGANISM(S): Homo sapiens

SUBMITTER: Daniel Salomon

PROVIDER: E-GEOD-58684 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [RNA-Seq]

Project description:Memory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human naïve and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to naïve cells, revealing specific genes more rapidly expressed in memory compared to naïve cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression. RNA sequencing of primary human naïve and memory CD4 T cells at rest and 48 hours post-activation.

2015-01-20 | E-GEOD-59846 | biostudies-arrayexpress

Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [Bisulfite-Seq]

Project description:Memory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human naïve and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to naïve cells, revealing specific genes more rapidly expressed in memory compared to naïve cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression. Targeted bisulfite sequencing of primary human naïve and memory CD4 T cells at rest and 48 hours post-activation.

2015-01-20 | E-GEOD-59858 | biostudies-arrayexpress

A Multi-Omic Analysis of Human Naive CD4 T cells

Project description:Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel measurements across thousands of genes and gene products. Such high-throughput technologies have been extensively used to carry out genome-wide studies particularly in the context of diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome, and proteome of a single mammalian cell type to obtain a coherent view of the complex interplay between omes has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells, revealing hundreds of unannotated mRNA transcripts, miRNAs, pseudogenes, and noncoding RNAs. Additionally, we carried out a comparative analysis of naïve CD4+ T cells with primary resting memory CD4+ T cells, which have provided novel insights into T cell biology. Overall, our data will serve as a baseline reference of a single pure population of cells for future systems level analysis of other defined cell populations.

2015-11-12 | PXD000376 | Pride

Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [Bisulfite-Seq]

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Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [RNA-Seq]

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Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [Affymetrix]

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Gene expression by human splenic B-cell subsets

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2012-05-12 | E-GEOD-32901 | biostudies-arrayexpress

Promoter H3K4 methylation reveals the dynamic reinforcement of activation-induced pathways in human CD4 T cells with differential kinetics in naÃ¯ve and memory cells (RNA-Seq)

Project description:The epigenetic determinants driving the rapid responses of memory CD4 T cells to antigen are currently an area of active research. While much has been done to characterize various Th subsets and their associated genome-wide epigenetic patterns, the dynamics of histone modifications during CD4 T cell activation and the differential kinetics of these epigenetic marks between naÃ¯ve and memory T cells have not been evaluated. In this study we have detailed the dynamics of genome-wide promoter H3K4me2 and H3K4me3 over a time course during activation of human naÃ¯ve and memory CD4 T cells. Our results demonstrate that changes to H3K4 methylation predominantly occur relatively late after activation (120 hours) and reinforce activation-induced upregulation of gene expression affecting multiple pathways important to T cell activation, differentiation, and function. The dynamics and mapped pathways of H3K4 methylation are distinctly different in memory cells. Memory CD4 have substantially more promoters marked by H3K4me3 alone, and that is influenced by promoter CpG content, reinforcing their more differentiated state. Our study provides the first data examining genome-wide histone modification dynamics during T cell activation, providing insight into the cross-talk between H3K4 methylation and gene expression, and underscoring the impact of these marks upon key pathways integral to CD4 T cell activation and function. RNA-Seq of naÃ¯ve and memory CD4 T cells at rest and at 3 time points after activation with anti-CD3/CD28.

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Influence of Interferon-beta on expression profile of memory T-cells

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2012-12-01 | E-GEOD-35601 | biostudies-arrayexpress

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