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EpiChip: Gene-by-gene quantification of epigenetic modification levels

ABSTRACT: Using datasets for the H3KAc histone modification in Th2 cells and an accompanying IgG control, we present an analysis strategy termed 'EpiChip' that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal.

ORGANISM(S): Mus musculus

PROVIDER: GSE23092 | GEO | 2010/12/07

SECONDARY ACCESSION(S): PRJNA131877

REPOSITORIES: GEO

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EpiChip: Gene-by-gene quantification of epigenetic modification levels

Project description:Using datasets for the H3KAc histone modification in Th2 cells and an accompanying IgG control, we present an analysis strategy termed 'EpiChip' that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal. Examination of H3KAc histone modifications in one cell type plus an IgG control.

2010-12-07 | E-GEOD-23092 | biostudies-arrayexpress

EpiChIP: gene-by-gene quantification of epigenetic modification levels.

Project description:The combination of chromatin immunoprecipitation with next-generation sequencing technology (ChIP-seq) is a powerful and increasingly popular method for mapping protein-DNA interactions in a genome-wide fashion. The conventional way of analyzing this data is to identify sequencing peaks along the chromosomes that are significantly higher than the read background. For histone modifications and other epigenetic marks, it is often preferable to find a characteristic region of enrichment in sequencing reads relative to gene annotations. For instance, many histone modifications are typically enriched around transcription start sites. Calculating the optimal window that describes this enrichment allows one to quantify modification levels for each individual gene. Using data sets for the H3K9/14ac histone modification in Th cells and an accompanying IgG control, we present an analysis strategy that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal. Curve fitting permits false discovery rate-based classification of genes as modified versus unmodified. We have developed a software package called EpiChIP that carries out this type of analysis, including integration with and visualization of gene expression data.

| S-EPMC3061070 | biostudies-literature

Gene expression changes in C57Bl/6 and CD16-/- murine bone-marrow derived dendritic cells (BMDCs) following overnight stimulation with OVA or OVA-immune complex

Project description:Atopic asthma is a chronic inflammatory disease of the lungs that is commonly associated with a Th2 response. The role of allergen-specific IgG in the initiation and development of allergic airway inflammation is still poorly understood; however, a receptor of IgG-immune complexes, CD16, has been demonstrated to promote augmentation of Th2 responses. To identify what genes downstream of CD16 signaling may be contributing to development of a Th2 response, we use ovalbumin (OVA) as our model antigen and compared wildtype and CD16-/- BMDCs that were treated overnight with OVA or OVA-immune complex.

2013-02-20 | GSE44388 | GEO

Gene expression changes in C57Bl/6 and CD16-/- murine bone-marrow derived dendritic cells (BMDCs) following overnight stimulation with OVA or OVA-immune complex

2013-02-20 | E-GEOD-44388 | biostudies-arrayexpress

Histone modification levels are predictive for gene expression.

Project description:Histones are frequently decorated with covalent modifications. These histone modifications are thought to be involved in various chromatin-dependent processes including transcription. To elucidate the relationship between histone modifications and transcription, we derived quantitative models to predict the expression level of genes from histone modification levels. We found that histone modification levels and gene expression are very well correlated. Moreover, we show that only a small number of histone modifications are necessary to accurately predict gene expression. We show that different sets of histone modifications are necessary to predict gene expression driven by high CpG content promoters (HCPs) or low CpG content promoters (LCPs). Quantitative models involving H3K4me3 and H3K79me1 are the most predictive of the expression levels in LCPs, whereas HCPs require H3K27ac and H4K20me1. Finally, we show that the connections between histone modifications and gene expression seem to be general, as we were able to predict gene expression levels of one cell type using a model trained on another one.

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Priming for Th2 differentiation requires IL-2-mediated induction of IL-4 receptor alpha chain expression

Project description:Th2 cells enable humoral immunity and host-defense to parasites. Whereas IL-4 drives Th2 differentiation and IL-2 is important later in this process by augmenting IL4 chromatin accessibility, we demonstrate that IL-2 serves an essential early role in regulating IL-4R? expression by inducing binding of Stat5a and Stat5b to the IL4ra locus, with sustained binding during Th2 differentiation. Although IL-4 induces IL-4R? expression, TCR-induced IL-4R? expression was unexpectedly normal in ILr-/- but profoundly diminished in IL2-/- T cells. Remarkably, enforced IL-4R? expression rescued Th2 differentiation in IL2-/- cells. These results reveal a novel function for IL-2, with IL-2 via Stat5 providing an early signal for IL4ra induction, thereby priming cells for Th2 differentiation and promoting/maintaining IL-4R? expression in Th2-committed cells. ChIP-seq experiments for Stat5a and Stat5b with an IgG control experiment for 8hr, 13hr and 2 rounds of Th2 differentiation. Keywords: ChIP-seq, Illumina, Th2 differentiation, Stat ChIP-seq experiments for Stat5a and Stat5b with an IgG control experiment for 8hr, 13hr and 2 rounds of Th2 differentiation. There are a total of 22 lanes of data for the three samples across the three time points.

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Expression data from different levels of anti-CD4 in HIV+ people

Project description:HIV-infected subjects were stratified to two groups high IgG anti-CD4 antibodies and low IgG anti-CD4 antibodies on day 14 (D14) after (“high” ≥ 2-fold increase from baseline; “low” < 2-fold increase)

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Priming for Th2 differentiation requires IL-2-mediated induction of IL-4 receptor alpha chain expression

Project description:Th2 cells enable humoral immunity and host-defense to parasites. Whereas IL-4 drives Th2 differentiation and IL-2 is important later in this process by augmenting IL4 chromatin accessibility, we demonstrate that IL-2 serves an essential early role in regulating IL-4Rα expression by inducing binding of Stat5a and Stat5b to the IL4ra locus, with sustained binding during Th2 differentiation. Although IL-4 induces IL-4Rα expression, TCR-induced IL-4Rα expression was unexpectedly normal in ILr-/- but profoundly diminished in IL2-/- T cells. Remarkably, enforced IL-4Rα expression rescued Th2 differentiation in IL2-/- cells. These results reveal a novel function for IL-2, with IL-2 via Stat5 providing an early signal for IL4ra induction, thereby priming cells for Th2 differentiation and promoting/maintaining IL-4Rα expression in Th2-committed cells. ChIP-seq experiments for Stat5a and Stat5b with an IgG control experiment for 8hr, 13hr and 2 rounds of Th2 differentiation. Keywords: ChIP-seq, Illumina, Th2 differentiation, Stat

2008-12-11 | GSE12346 | GEO

Gene expression changes accompanying vascular tortuosity

Project description:Gene expression changes accompanying vascular tortuosity

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Baseline Chromatin Modification Levels May Predict Interindividual Variability in Ozone-Induced Gene Expression.

Project description:Traditional toxicological paradigms have relied on factors such as age, genotype, and disease status to explain variability in responsiveness to toxicant exposure; however, these are neither sufficient to faithfully identify differentially responsive individuals nor are they modifiable factors that can be leveraged to mitigate the exposure effects. Unlike these factors, the epigenome is dynamic and shaped by an individual's environment. We sought to determine whether baseline levels of specific chromatin modifications correlated with the interindividual variability in their ozone (O3)-mediated induction in an air-liquid interface model using primary human bronchial epithelial cells from a panel of 11 donors. We characterized the relationship between the baseline abundance of 6 epigenetic markers with established roles as key regulators of gene expression-histone H3 lysine 4 trimethylation (H3K4me3), H3K27 acetylation (H3K27ac), pan-acetyl H4 (H4ac), histone H3K27 di/trimethylation (H3K27me2/3), unmodified H3, and 5-hydroxymethylcytosine (5-hmC)-and the variability in the O3-induced expression of IL-8, IL-6, COX2, and HMOX1. Baseline levels of H3K4me3, H3K27me2/3, and 5-hmC, but not H3K27ac, H4ac, and total H3, correlated with the interindividual variability in O3-mediated induction of HMOX1 and COX2. In contrast, none of the chromatin modifications that we examined correlated with the induction of IL-8 and IL-6. From these findings, we propose an "epigenetic seed and soil" model in which chromatin modification states between individuals differ in the relative abundance of specific modifications (the "soil") that govern how receptive the gene is to toxicant-mediated cellular signals (the "seed") and thus regulate the magnitude of exposure-related gene induction.

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