DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Barter, M.J.; Bui, Catherine; Cheung, Kathleen; Falk, Julia; Gómez, Rodolfo; Skelton, Andrew; Elliott, Hannah R; Reynard, Louise N.; Young, David A.

doi:10.1038/s41598-020-58093-5

Cited by 22 publications

(21 citation statements)

References 60 publications

(87 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An Infinium HumanMethylation450 BeadChip array was used to quantify DNA methylation in the Transwell model of chondrogenesis, GEO dataset http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129266. CpG probes from the 450K methylation array were based on human reference genome hg19; therefore, CpG coordinates from the array were first converted to hg38 and intersected with chromatin state coordinates from hMSC and differentiated chondrocytes.…”

Section: Methodsmentioning

confidence: 99%

“…DNA methylation changes during the in vitro Transwell model of chondrogenesis were largely demethylation events that were associated with chondrogenesisrelated GO terms. 36 We integrated the DNA methylation and ChIP-seq data in order to investigate the DNA methylation changes in chromatin states during MSC chondrogenesis, focusing on the hypomethylated CpGs (94% of the significantly differentially methylated loci during chondrogenesis) since this is linked to gene transcription activation. Global methylation patterns reflect known trends ( Figure 5A,B), for example, gene promoters tend to have low percentage methylation relative to the rest of the genome.…”

Section: Dna Methylation At Gene Enhancersmentioning

confidence: 99%

See 1 more Smart Citation

Histone ChIP‐Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell‐type specificity

et al. 2020

Self Cite

View full text Add to dashboard Cite

Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the 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 posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP‐seq and cis‐regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis‐related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de‐methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell‐types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell‐types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross‐talk between different epigenetic mechanisms during chondrocyte differentiation.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Dna Methylation At Gene Enhancersmentioning

confidence: 99%

Histone ChIP‐Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell‐type specificity

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…An Illumina Infinium HumanMethylation450K BeadChip array was used to measure DNA methylation. DNA methylation changes during the in vitro transwell model of chondrogenesis were largely de-methylation events which were associated with chondrogenesis related GO terms [27]. We integrated the DNA methylation and ChIP-seq data in order to investigate the DNA methylation changes in chromatin states during MSC chondrogenesis, focusing on the hypomethylated CpGs (94% of the significantly differentially methylated loci during chondrogenesis) since this is linked to gene transcription activation.…”

Section: Dna Methylation At Gene Enhancersmentioning

confidence: 99%

“…An Infinium HumanMethylation450 BeadChip array was used to quantify DNA methylation in the transwell model of chondrogenesis [27], GEO dataset GSE129266. CpG probes from the 450k methylation array were based on human reference genome hg19, therefore, CpG coordinates from the array were first converted to hg38 and intersected with chromatin state co-ordinates from hMSC and differentiated chondrocytes.…”

Section: Integration With Dna Methylationmentioning

confidence: 99%

Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity

Cheung

Barter

Falk

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Human mesenchymal stem cells are able to differentiate into chondrocytes, the cell type found in cartilage, making them an accessible system to study gene regulation during this process. Epigenetic mechanisms such as histone modifications and DNA methylation together with transcription factor binding play a role in activating and repressing gene expression. In this study, we investigated the genome-wide histone modification changes during chondrocyte differentiation. Integration of this data with DNA methylation and SOX9 transcription factor ChIP-seq revealed epigenetic changes at gene enhancer elements.Regions of the genome that transition from non-enhancers to enhancers in chondrocytes are enriched for SOX9 transcription factor binding sites. Luciferase reporter assays revealed that enhancer activity may be modulated by manipulating DNA methylation and SOX9 expression.This study has defined important regulatory elements in chondrocytes which could serve as targets for future mechanistic studies. AbstractEpigenetic 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. Chondrocyte enhancers were associated with chondrogenesis related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de-methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this studywith epigenomes of cell-types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell-types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers.Luciferase reporter assays confirmed that chondrocyte enhancers characterised in this study exhibited enhancer activity which may be modulated by inducing DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross-talk between different epigenetic mechanisms during chondrocyte differentiation.

show abstract

“…Though DNA methylation is the most well characterised epigenetic mark, changes in gene expression correlate poorly with methylation alterations at promoters, and instead methylation changes tend to occur in regions of the genome defined as transcriptional enhancers [2]. Furthermore, although methyl groups at CpG loci can be both added and removed, the processes involved are not very dynamic, especially active demethylation which requires a series of enzymatic modifications to 5methylcytosine (5mC) by so-called TET-TDG pathway coupled with base excision repair (BER) [3].…”

Section: Introductionmentioning

confidence: 99%

Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

Barter

Cheung

Falk

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Genome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome. Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed.Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions for that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model.Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.

show abstract

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Cited by 22 publications

References 60 publications

Histone ChIP‐Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell‐type specificity

Histone ChIP‐Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell‐type specificity

Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity

Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

Contact Info

Product

Resources

About