Identification of differentially methylated regions in new genes associated with knee osteoarthritis

Gene

Volumn 576, Issue 1, 2016, Pages 312-318

  Bonin, Carolina A ^a   Lewallen, Eric A ^a   Baheti, Saurabh ^b   Bradley, Elizabeth W ^a   Stuart, Michael J ^a   Berry, Daniel J ^a   van Wijnen, Andre J ^a,c   Westendorf, Jennifer J ^a,c  

^a MAYO CLINIC   (United States)

^b Department of Biomedical Statistics and Informatics ^*  (United States)

^c MAYO GRADUATE SCHOOL   (United States)

Author keywords

Articular cartilage; Differentially methylated regions; DNA methylation; FOXP4; SHROOM1

Indexed keywords

BISULFITE; PROTEIN; PROTEIN SHROOM1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXP4; UNCLASSIFIED DRUG; ACTIN BINDING PROTEIN; AZACITIDINE; FORKHEAD TRANSCRIPTION FACTOR; FOXP4 PROTEIN, HUMAN; MEMBRANE PROTEIN; SHROOM1 PROTEIN, HUMAN;

ARTICLE; ARTICULAR CARTILAGE; BIOINFORMATICS; CELL CULTURE; CLINICAL ARTICLE; CONTROLLED STUDY; CPG ISLAND; DEMETHYLATION; DIFFERENTIALLY METHYLATED REGION; DNA EXTRACTION; DNA METHYLATION; DNA STRUCTURE; EXON; GENE ACTIVATION; GENE EXPRESSION; GENE REPRESSION; GENE SEQUENCE; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; KNEE OSTEOARTHRITIS; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; CHONDROCYTE; DRUG EFFECTS; GENETICS; PATHOLOGY; REFERENCE VALUE; REPRODUCIBILITY;

AZACITIDINE; CARTILAGE, ARTICULAR; CELLS, CULTURED; CHONDROCYTES; CPG ISLANDS; DNA METHYLATION; FORKHEAD TRANSCRIPTION FACTORS; HUMANS; MEMBRANE PROTEINS; MICROFILAMENT PROTEINS; OSTEOARTHRITIS, KNEE; PROMOTER REGIONS, GENETIC; REFERENCE VALUES; REPRODUCIBILITY OF RESULTS;

EID: 84951193169     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.10.037     Document Type: Article

References (37)

1. Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., et al. An atlas of active enhancers across human cell types and tissues. Nature 507 (2014), 455–461.
2. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25 (2000), 25–29.
3. Bell, J.T., Tsai, P.C., Yang, T.P., Pidsley, R., Nisbet, J., Glass, D., et al. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet. 8 (2012), 189–200.
4. Bock, C., Analysing and interpreting DNA methylation data. Nat. Rev. Genet. 13 (2012), 705–719.
5. Burr, D.B., Gallant, M.A., Bone remodelling in osteoarthritis. Nat. Rev. Rheumatol. 8 (2012), 665–673.
6. de Andres, M.C., Imagawa, K., Hashimoto, K., Gonzalez, A., Roach, H.I., Goldring, M.B., et al. Loss of methylation in CpG sites in the NF-kappaB enhancer elements of inducible nitric oxide synthase is responsible for gene induction in human articular chondrocytes. Arthritis Rheum. 65 (2013), 732–742.
7. Delgado-Calle, J., Fernandez, A.F., Sainz, J., Zarrabeitia, M.T., Sanudo, C., Garcia-Renedo, R., et al. Genome-wide profiling of bone reveals differentially methylated regions in osteoporosis and osteoarthritis. Arthritis Rheum. 65 (2013), 197–205.
8. den Hollander, W., Ramos, Y.F., Bomer, N., Elzinga, S., van der Breggen, R., Lakenberg, N., et al. Transcriptional associations of osteoarthritis-mediated loss of epigenetic control in articular cartilage. Arthritis Rheum. 67 (2015), 2108–2116.
9. Dietz, M.L., Bernaciak, T.M., Vendetti, F., Kielec, J.M., Hildebrand, J.D., Differential actin-dependent localization modulates the evolutionarily conserved activity of Shroom family proteins. J. Biol. Chem. 281 (2006), 20542–20554.
10. Fernandez-Tajes, J., Soto-Hermida, A., Vazquez-Mosquera, M.E., Cortes-Pereira, E., Mosquera, A., Fernandez-Moreno, M., et al. Genome-wide DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients. Ann. Rheum. Dis. 73 (2014), 668–677.
11. Goldring, M.B., The role of the chondrocyte in osteoarthritis. Arthritis Rheum. 43 (2000), 1916–1926.
12. Goldring, M.B., Goldring, S.R., Osteoarthritis. J. Cell. Physiol. 213 (2007), 626–634.
13. Goldring, M.B., Goldring, S.R., Articular cartilage and subchondral bone in the pathogenesis of osteoarthritis. Ann. N. Y. Acad. Sci. 1192 (2010), 230–237.
14. Goldring, M.B., Marcu, K.B., Cartilage homeostasis in health and rheumatic diseases. Arthritis Res. Ther., 11, 2009, 224.
15. Goldring, M.B., Marcu, K.B., Epigenomic and microRNA-mediated regulation in cartilage development, homeostasis, and osteoarthritis. Trends Mol. Med. 18 (2012), 109–118.
16. Hashimoto, K., Oreffo, R.O., Gibson, M.B., Goldring, M.B., Roach, H.I., DNA demethylation at specific CpG sites in the IL1B promoter in response to inflammatory cytokines in human articular chondrocytes. Arthritis Rheum. 60 (2009), 3303–3313.
17. Hashimoto, K., Otero, M., Imagawa, K., de Andres, M.C., Coico, J.M., Roach, H.I., et al. Regulated transcription of human matrix metalloproteinase 13 (MMP13) and interleukin-1beta (IL1B) genes in chondrocytes depends on methylation of specific proximal promoter CpG sites. J. Biol. Chem. 288 (2013), 10061–10072.
18. Hon, G.C., Hawkins, R.D., Caballero, O.L., Lo, C., Lister, R., Pelizzola, M., et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 22 (2012), 246–258.
19. Iliopoulos, D., Malizos, K.N., Tsezou, A., Epigenetic regulation of leptin affects MMP-13 expression in osteoarthritic chondrocytes: possible molecular target for osteoarthritis therapeutic intervention. Ann. Rheum. Dis. 66 (2007), 1616–1621.
20. Jeffries, M.A., Donica, M., Baker, L.W., Stevenson, M.E., Annan, A.C., Humphrey, M.B., et al. Genome-wide DNA methylation study identifies significant epigenomic changes in osteoarthritic cartilage. Arthritis Rheum. 66 (2014), 2804–2815.
21. Kim, K.I., Park, Y.S., Im, G.I., Changes in the epigenetic status of the SOX-9 promoter in human osteoarthritic cartilage. J. Bone Miner. Res. 28 (2013), 1050–1060.
22. Laird, P.W., Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet. 11 (2010), 191–203.
23. Lee, C., Le, M.P., Wallingford, J.B., The shroom family proteins play broad roles in the morphogenesis of thickened epithelial sheets. Dev. Dyn. 238 (2009), 1480–1491.
24. Mi, H.Y., Muruganujan, A., Thomas, P.D., PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41 (2013), D377–D386.
25. Moazedi-Fuerst, F.C., Hofner, M., Gruber, G., Weinhaeusel, A., Stradner, M.H., Angerer, H., et al. Epigenetic differences in human cartilage between mild and severe OA. J. Orthop. Res. 32 (2014), 1636–1645.
26. Reynard, L.N., Bui, C., Syddall, C.M., Loughlin, J., CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383. Hum. Genet. 133 (2014), 1059–1073.
27. Roach, H.I., Yamada, N., Cheung, K.S.C., Tilley, S., Clarke, N.M.P., Oreffo, R.O.C., et al. Association between the abnormal expression of matrix-degrading enzymes by human osteoarthritic chondrocytes and demethylation of specific CpG sites in the promoter regions. Arthritis Rheum. 52 (2005), 3110–3124.
28. Rushton, M.D., Reynard, L.N., Barter, M.J., Refaie, R., Rankin, K.S., Young, D.A., et al. Characterization of the cartilage DNA methylome in knee and hip osteoarthritis. Arthritis Rheum. 66 (2014), 2450–2460.
29. Song, F., Smith, J.F., Kimura, M.T., Morrow, A.D., Matsuyama, T., Nagase, H., et al. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc. Natl. Acad. Sci. U. S. A. 102 (2005), 3336–3341.
30. Song, F., Mahmood, S., Ghosh, S., Liang, P., Smiraglia, D.J., Nagase, H., et al. Tissue specific differentially methylated regions (TDMR): changes in DNA methylation during development. Genomics 93 (2009), 130–139.
31. Sun, Z., Baheti, S., Middha, S., Kanwar, R., Zhang, Y., Li, X., et al. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics 28 (2012), 2180–2181.
32. Ushijima, T., Innovation — detection and interpretation of altered methylation patterns in cancer cells. Nat. Rev. Cancer 5 (2005), 223–231.
33. Woolf, A.D., Pfleger, B., Burden of major musculoskeletal conditions. Bull. World Health Organ. 81 (2003), 646–656.
34. Xi, Y., Li, W., BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics, 10, 2009, 232.
35. Yelin, E.H., Cisternas, M., Watkins-Castillo, S.I., United States bone and joint initiative: the Burden of Musculoskeletal Diseases in the United States (BMUS). Medical Care Expenditures and Earnings Losses for Select Musculoskeletal Diseases, Third ed., 2014 http://www.boneandjointburden.org/about/rights (Rosemont, IL).
36. Zhao, H.X., Zhou, W.R., Yao, Z.J., Wan, Y., Cao, J.J., Zhang, L.L., et al. Foxp1/2/4 regulate endochondral ossification as a suppresser complex. Dev. Biol. 398 (2015), 242–254.
37. Ziller, M.J., Gu, H., Muller, F., Donaghey, J., Tsai, L.T., Kohlbacher, O., et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500 (2013), 477–481.