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Monocyte-to-macrophage differentiation is defined by gain and loss of DNA methylation at transcription factor binding sites

ABSTRACT: Monocyte-to-macrophage differentiation is defined by gain and loss of DNA methylation at transcription factor binding sites

PROVIDER: PRJNA486502 | ENA |

REPOSITORIES: ENA

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Monocyte-to-macrophage differentiation is defined by gain and loss of DNA methylation at transcription factor binding sites

Project description:Macrophages and their precursors monocytes play a key role in inflammation and chronic inflammatory disorders. Monocyte-to-macrophage differentiation and activation programs are accompanied by significant epigenetic remodeling where DNA methylation associates with cell development and identity. Here we show that confined local gain and loss of DNA methylation at transcription factor binding sites as a key characteristic of macrophage identity. Using the Illumina 450k array with a paired epigenome-wide analysis in combination with public whole-genome sequencing data we found that differential DNA methylation was typically highly localized to single CpGs or very short regions that are enriched for lineage specific enhancers. Furthermore, differentially methylated CpGs were located at sites characterized by increased binding of transcription factors known to be involved in monocyte-to-macrophage differentiation including C/EBP and ETS for gain and AP-1 for loss-of-methylation. Our study highlights subtle, highly localized remodeling of DNA methylation at regulatory regions as key in understanding cell differentiation and, potentially, disease mechanisms.

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Regulation of Activation-Associated MicroRNA Accumulation Rates during Monocyte-to-Macrophage Differentiation

Project description:We profiled miRNA expression using TaqMan TLDA assays to identify miRNAs with expression levels that were affected by differences in culturing conditions during monocyte-to-macrophage differentiation. 9 samples: 3 sample types for 3 different human donors

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Human monocyte derived macrophage microarray analysis

Project description:Microarray data was acquired from human primary monocyte-derived macrophages in order to test the validity of a graphical software package (z-score outlier detection (ZODET)) Complex human diseases can show significant heterogeneity between patients with the same phenotypic disorder. An outlier detection strategy was developed to identify variants at the level of gene transcription that are of potential biological and phenotypic importance. Here we describe a graphical software package (z-score outlier detection (ZODET)) that enables identification and visualisation of gross abnormalities in gene expression (outliers) in individuals, using whole genome microarray data. Mean and standard deviation of expression in a healthy control cohort is used to detect both over and under-expressed probes in individual test subjects. We compared the potential of ZODET to detect outlier genes in gene expression datasets with a previously described statistical method, gene tissue index (GTI), using a simulated expression dataset and a publicly available monocyte-derived macrophage microarray dataset. Taken together, these results support ZODET as a novel approach to identify outlier genes of potential pathogenic relevance in complex human diseases. The algorithm is implemented using R packages and java. 40 volunteer were bled and primary monocyte derived macrophages were cultured. These samples were then randomised into two equal sized groups (control - A1-20 and experimental - B1-20) and run on the ZODET software.

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Regulation of Activation-Associated Transcripts Accumulation Rates during Monocyte-to-Macrophage Differentiation

Project description:We profiled macrophage activation-associated transcripts using TaqMan assays in a Fluidigm 48.48 Gene Expression Array to identify transcripts with expression levels that were affected by differences in culturing conditions during monocyte-to-macrophage differentiation.

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Epigenetic dynamics of monocyte to macrophage differentiation

Project description:Monocyte to macrophage differentiation involves major biochemical and structural changes in non-dividing cells. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were isolated by elutriation and differentiated in vitro by addition of MCSF in serum-free medium. We also investigated the effect of loading the macrophages with modified LDL. We found that many mRNAs and miRNAs were significantly up- or downregulated during differentiation. While there was no correlation between gene expression and DNA methylation changes at transcription start sites, we identified a large number of intra- and intergenic regions that rapidly lost DNA methylation, became nucleosome-free and gained histone marks indicative of active enhancers. Loading of macrophages with modified LDL caused gene expression changes, but no chromatin changes. In summary, our results demonstrate that monocyte to macrophage differentiation is associated with rapid, highly targeted epigenetic changes, whereas lipid uptake mainly affects regulatory circuits of soluble factors.

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Regulation of Activation-Associated MicroRNA Accumulation Rates during Monocyte-to-Macrophage Differentiation

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