Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

Liu, Ye; Chang, Jen-Chien; Hon, Chung-Chau; Fukui, Naoshi; Tanaka, Nobuhiro; Zhang, Zhen Ya; Lee, Ming Ta Michael; Minoda, Aki

doi:10.1038/s41598-018-33779-z

Cited by 42 publications

(50 citation statements)

References 88 publications

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“…Interestingly the converse is also true whereby binding of transcription factors to promoters even in the absence of active transcription can cause the local loss of DNA methylation (Edwards et al , 2017). To better establish correlation whole genome methylation in combination with chondrocyte ATAC-seq data with gene expression and possible overlap of methylation and transcription factor binding sites (Liu et al , 2018).…”

Section: Discussionmentioning

confidence: 99%

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Barter

Bui

Cheung

et al. 2019

Preprint

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SummaryRegulation of transcription occurs in a cell type specific manner by epigenetic mechanisms including DNA methylation and histone modifications. Methylation changes during stem cell differentiation may play a key role in lineage specification. We sought to characterise DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) in order to further our understanding of epigenetic regulation in chondrocytes. 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. We identified significant DNA hypomethylation during chondrogenesis including changes at many key cartilage gene loci. Importantly characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with adult cartilage and other tissue methylation profiles identified chondrocyte-specific regulatory regions. Taken together we have associated methylation at many CpGs with the chondrocyte phenotype.AbstractRegulation of transcription is determined in a cell type specific manner by epigenetic mechanisms including DNA methylation and histone modifications. Methylation changes during stem cell differentiation may play a role in lineage specification. Multipotent mesenchymal stem cell (MSC) differentiation into chondrocytes not only serves as a model for chondrocyte development but also provides an important source of cartilage for tissue engineering purposes. We sought to characterise DNA methylation changes during chondrogenesis to further understanding of epigenetic regulation but to also provide context for the changes identified during disease.DNA cytosine methylation changes during human MSC differentiation into chondrocytes were measured by Infinium 450K methylation array. Methylation changes at gene loci were contrasted with gene expression changes. Chromatin states of significant methylation loci were interpreted by intersection with chondrogenesis histone modification ChlP-seq data. Chondrogenic and cartilage specific hypomethylation was utilised in order to identify a chondrocyte methylome. Articular cartilage and tissue panel DNA methylation was compared and alterations during osteoarthritis cartilage disease classified.Significant DNA hypomethylation was identified following chondrogenic differentiation of MSCs including changes at many key cartilage gene loci. Highly upregulated genes during chondrogenesis were more likely to exhibit a reduction in DNA methylation. Characterisation of significant CpG loci indicated their predominant localisation in CpG poor regions which importantly are most likely to correspond to enhancer regions. Methylation level at certain CpGs following chondrogenesis corresponds to the level found in adult cartilage.Taken together, considerable demethylation changes to the epigenetic landscape occur during MSC chondrogenesis especially at sites marked by enhancer modifications. Comparison with other tissues, including healthy and OA cartilage, associates CpGs to the chondrocyte phenotype and provides context for changes in disease.

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Section: Discussionmentioning

confidence: 99%

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Barter

Bui

Cheung

et al. 2019

Preprint

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“…0.8 (referred to the LD class in 28 ) of the OA variant calculated by LDlink 48 using the 1,000 Genomes Project phase three data 49 in the same population(s) as the GWAS study; other traits: loci also significantly associated with height (He, 28 ), bone area (BA, 39 ), hip shape (HS, 36 ) and developmental dysplasia of the hip (DDH, 37 ); AI: overlap of all DNA variants within the LD class and transcript SNPs from 52 showing significant allelic imbalance (AI) in cartilage. The effect of the OA risk allele on gene expression is shown ([ ¼ increased and Y ¼ decreased); ATACseq SNPs: number of DNA variants within the LD class that overlap ATACseq peaks in cartilage identified in 77 . The ATACseq peaks in hg38 were lifted over into hg19 using the UCSC LiftOver tool and overlapped with OA DNA variants using the UCSC Data Integrator tool.…”

Section: Functional Studies Of Oa Locimentioning

confidence: 99%

“…Techniques used for the latter analyses, namely chromatin immunoprecipitation sequencing (ChIPseq) and DHS mapping, have previously required unfeasibly large number of freshly isolated cells (typically 1 Â 10 6 to 2 Â 10 7 cells), preventing such studies in cartilage. However, this has changed within the last year with publication of the first reports of histone ChIPseq and mapping of open chromatin regions in human chondrocytes 57,77 .…”

Section: Genome-wide Mapping Of Open Chromatin and Histone Modificationsmentioning

confidence: 99%

“…In the second study 77 , the open chromatin regions of preserved and damaged regions of knee cartilage from eight OA patients were mapped using the assay for transposase-accessible chromatin using sequencing (ATACseq; 78 ). This is a fast and sensitive alternative method to DHS mapping that requires 5,000 to 50,000 cells, making analysis of cartilage and other primary joint tissues feasible.…”

Section: Genome-wide Mapping Of Open Chromatin and Histone Modificationsmentioning

confidence: 99%

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Osteoarthritis year in review 2019: genetics, genomics and epigenetics

Reynard

Barter

2020

Osteoarthritis and Cartilage

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s u m m a r yAlthough osteoarthritis (OA) aetiology is complex, genetic, genomic and epigenetic studies published within the last decade have advanced our understanding of the molecular processes underlying this common musculoskeletal disease. The purpose of this narrative review is to highlight the key research articles within the OA genetics, genomics and epigenetics fields that were published between April 2018 and April 2019. The review focuses on the identification of new OA genetic risk loci, genomics techniques that have been used for the first time in human cartilage and new publicly available databases, and datasets that will aid OA functional studies.Fifty-six new OA susceptibility loci were identified by two large scale genome wide association study meta-analyses, increasing the number of genome-wide significant risk loci to 90. OA risk variants are enriched near genes involved in skeletal development and morphology, and show genetic overlap with height, hip shape, bone area and developmental dysplasia of the hip. Several functional studies of OA loci were published, including a genome-wide analysis of genetic variation on cartilage gene expression. A specialised data portal for exploring cross-species skeletal transcriptomic datasets has been developed, and the first use of cartilage single cell RNAseq analysis reported. This year also saw the systematic identification of all microRNAs, long non-coding RNAs and circular RNAs expressed in human OA cartilage. Putative transcriptional regulatory regions have been mapped in human chondrocytes genome-wide, providing a dataset that will facilitate the prioritisation and characterisation of OA genetic and epigenetic loci.

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“…Routinely, 5-10 µM tissue sections are used for immunopathological and other staining analysis. Currently, ATAC-seq method for chromatin accessibility studies requires 50,000 purified nuclei from patient brain and cartilage tissue samples (7,9). Indeed, 20 mgs of brain tissue samples were used from post-mortem human brain samples for nuclei preparation (7).…”

Section: Universal Nice-seq Of Human 5-10 µM Frozen Tissue Sectionsmentioning

confidence: 99%

Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues

Chin

Sun²,

Vishnu³

et al. 2020

Preprint

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Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.

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Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

Cited by 42 publications

References 88 publications

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Osteoarthritis year in review 2019: genetics, genomics and epigenetics

Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues

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