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Characterisation of DNA methylation during mesenchymal stem cell chondrogenesis

ABSTRACT: Characterisation of DNA methylation during mesenchymal stem cell chondrogenesis

PROVIDER: PRJNA530691 | ENA |

REPOSITORIES: ENA

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Characterisation of DNA methylation during mesenchymal stem cell chondrogenesis

Project description:Regulation of transcription occurs in a cell type specific manner orchestrated by epigenetic mechanisms including DNA methylation. Methylation changes may also play a key role in lineage specification during stem cell differentiation. To further our understanding of epigenetic regulation in chondrocytes we characterised DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) by Infinium 450K methylation array. Significant DNA hypomethylation was identified during chondrogenesic differentiation including changes at many key cartilage gene loci. Integration with chondrogenesis gene expression data revealed an enrichment of significant CpGs in upregulated genes, while characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with methylation profiles of other tissues, including healthy and diseased adult cartilage, identified chondrocyte-specific regions of hypomethylation and the overlap with differentially methylated CpGs in osteoarthritis. Taken together we have associated DNA methylation levels with the chondrocyte phenotype. The consequences of which has potential to improve cartilage generation for tissue engineering purposes and also to provide context for observed methylation changes in cartilage diseases such as osteoarthritis

2019-05-24 | GSE129266 | GEO

Characterisation of epigenomic changes during chondrogenesis

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Characterisation of epigenomic changes during chondrogenesis

Project description:Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterised the epigenome during in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) was used to assess a range of N-terminal post-transcriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterised using histone ChIP-seq and cis-regulatory elements were identified in chondrocytes.

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Influence of DNA-methylation at multiple stages of limb chondrogenesis

Project description:Limb development is a well-established model for understanding cell fate decisions, and the formation of skeletal elements is coordinated through a sequence of events that control chondrogenesis spatiotemporally. It has been established that epigenetic control participates in cartilage maturation. Our research has shown for the first time that the inhibition of DNA methylation in interdigital tissue with 5-azacytidine results in the formation of an ectopic digit. This discovery suggested that DNA methylation dynamics could regulate the fate of cells between chondrogenesis and cell death during autopod development. We sequenced WGBS libraries from in-vivo interdigital tissue treated with 5-azacytidine or DMSO to identify genome-wide methylation changes during the early stages of 5-azacytidine-induced chondrogenesis.

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High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

Project description:Cartilage tissue engineering seeks to replace degenerated or damaged cartilage following disease or injury. Mesenchymal stem/stromal cells (MSCs) provide an attractive cell source for cartilage repair; however, the underlying molecular pathways that drive chondrogenesis of these pools of adult stem cells remains poorly understood. Here, we generated a rich data set of high throughput RNA sequencing of human MSCs throughout chondrogenesis at six different time points. Our data is consisted of 18 libraries with three individual donors as biological replicates, each library possessing a sequencing depth of 100 million reads. We also performed flow cytometric, histological, and biochemical analyses in parallel to validate the quality of our in vitro engineered cartilage. Differential gene expression and gene ontology analyses identified dynamic changes in multiple biological pathways, namely downregulation in cell cycle and proliferation, and upregulation in extracellular matrix synthesis. Weighted gene correlation network analysis also identified an important chondrogenic gene subset, whose functional characterization promises to further harness the potential of MSCs for cartilage tissue engineering. Furthermore, we created a graphic user interface encyclopedia built with the goal of producing an open resource of transcriptomic regulation for additional data-mining and pathway analysis of the process of MSC chondrogenesis. The tool can be accessed at: http://msc-browser.guilaklab.com

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