Chromatin accessibility in MSC chondrogenesis, adult hip cartilage chondrocytes and osteoarthritis

OBJECTIVE: Cell type-specific gene expression programs are mediated by interactions between enhancers, transcription factors and gene promoters. Access to the DNA is regulated by the presence and modification state of chromatin. This study sought to reveal the chromatin accessibility of the cartilage chondrocyte genome and identify changes that occur in accessibility during both development from mesenchymal stem cells (MSC) and in osteoarthritis (OA). METHOD: Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) was performed on bone-marrow-MSC and MSC-derived differentiated chondrocytes, as well as primary chondrocytes isolated from 16 patients undergoing total hip replacement because of OA or due to a neck of femur fracture. RESULTS: During MSC chondrogenesis we identified 138,005 open chromatin regions, with 20,979 regions undergoing increased accessibility. De novo established accessible regions were enriched at enhancer regions, defined previously by ChIP-seq, with key cartilage genes experiencing substantial chromatin reconfiguration often overlapping with SOX9 binding sites. In hip chondrocytes we identified 115,295 open chromatin regions, of which 1383 and 573 were more or less differentially accessible in OA. Comparison with a single cell ATAC-seq ATLAS identified accessible regions restricted to chondrocytes and established during chondrogenesis. Accessible regions were mapped to 320 OA-associated single nucleotide variants, many of which become accessible during chondrocyte development. CONCLUSIONS: This study illustrates the establishment of the chondrocyte chromatin landscape and identifies enhancer regions correlated with the cartilage transcriptome and associated with variants linked with cartilage disease OA.