Genome-wide DNA methylation profile implicates potential cartilage regeneration at the late stage of knee osteoarthritis Y. Zhang, N. Fukui, M. Yahata,

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Genome-wide DNA methylation profile implicates potential cartilage regeneration at the late stage of knee osteoarthritis Y. Zhang, N. Fukui, M. Yahata, Y. Katsuragawa, T. Tashiro, S. Ikegawa, M.T. Michael Lee Osteoarthritis and Cartilage Volume 24, Issue 5, Pages 835-843 (May 2016) DOI: 10.1016/j.joca.2015.12.013 Copyright © 2016 Osteoarthritis Research Society International Terms and Conditions

Fig. 1 Genome-wide DNA methylation profile in knee OA chondrocyte. (A) Heatmap of the 519 significant DMPs identified in iMT (inner medial tibia)/oLT (inner lateral tibia) comparison group. Vertical axis: the dendrogram showing the clusters of DMPs, horizontal axis: samples from the oLT and iMT regions. The methylation scales are shown on the top of the heatmap (0 = no methylation, 1 = 100% methylation). (B) Summary of the DMPs in the iMT/oLT group. The positive red bars indicate hypermethylation, the negative green bars hypomethylation. The Y-axis indicates the frequency of hyper- and hypomethylation. Frequency was illustrated at the end of each bar. The X-axis indicates the groups of |△β| values. (C) β value plot of selected examples from top DMPs. Osteoarthritis and Cartilage 2016 24, 835-843DOI: (10.1016/j.joca.2015.12.013) Copyright © 2016 Osteoarthritis Research Society International Terms and Conditions

Fig. 2 Pathway and genome feature analysis of the identified DM genes. (A) Gene ontology pathway analysis of the 519 DMPs. P-values are Benjamini-corrected for multiple tests. P≤: *, 0.05; **, 0.01; ***, 0.001. (B) Genome features of identified significant DMPs. The Y-axis: each genome feature, the X-axis: the percentage differences between the DMPs and array probes. Increased features are in solid bars, and decreased features in blank bars. DHS: DNase I hypersensitive sites. Enhancer: a short region of DNA (50–1500 bp) that can bind with transcription factors to activate transcription. Island: >200 bp with GC percentage >50% and observed/expected CpG ratio >60%. Shore: up to 2 kb from CpG island. Shelf: 2–4 kb from CpG island. OpenSea: isolated CpGs in the genome. Osteoarthritis and Cartilage 2016 24, 835-843DOI: (10.1016/j.joca.2015.12.013) Copyright © 2016 Osteoarthritis Research Society International Terms and Conditions

Fig. 3 Predicted pathways associated with DM genes. Red: hyper-methylated, blue: hypo-methylated. (A) Network 1 indicates the enrichment of homeobox genes (red arrows) and the signaling pathway centered on NF-κB complex. (B) Network two illustrates the involvement of extracellular molecules (red arrows). The signaling pathway centered on ERK1/2. Osteoarthritis and Cartilage 2016 24, 835-843DOI: (10.1016/j.joca.2015.12.013) Copyright © 2016 Osteoarthritis Research Society International Terms and Conditions