Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes

Arthritis and Rheumatology

Volumn 67, Issue 8, 2015, Pages 2129-2140

  Taylor, Sarah E B ^a   Li, Ye Henry ^a   Wong, Wing H ^a   Bhutani, Nidhi ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; DNA; CYTOSINE; MESSENGER RNA;

ADULT; AGED; ANTERIOR CRUCIATE LIGAMENT RECONSTRUCTION; ARTICLE; CARTILAGE CELL; CHILD; COL11A1 GENE; CONTROLLED STUDY; DNA HYDROXYMETHYLATION; DNA METHYLATION; EPIGENETICS; GAIN OF FUNCTION MUTATION; GDF5 GENE; GENE; GENE ACTIVATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE MAPPING; GENE REPRESSION; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; LOSS OF FUNCTION MUTATION; LRP5 GENE; MMP3 GENE; NUCLEOTIDE SEQUENCE; OSTEOARTHRITIS; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SURGICAL PATIENT; TOTAL KNEE REPLACEMENT; ARTICULAR CARTILAGE; CASE CONTROL STUDY; DNA SEQUENCE; GENETIC EPIGENESIS; GENETICS; INFANT; KNEE OSTEOARTHRITIS; METABOLISM; MIDDLE AGED;

ADULT; AGED; CARTILAGE, ARTICULAR; CASE-CONTROL STUDIES; CHONDROCYTES; CYTOSINE; DNA; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; HUMANS; INFANT; MIDDLE AGED; OSTEOARTHRITIS, KNEE; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

EID: 84938099956     PISSN: 23265191     EISSN: 23265205     Source Type: Journal    
DOI: 10.1002/art.39179     Document Type: Article

References (50)

1. Aigner T, Richter W., OA in 2011: age-related OA-a concept emerging from infancy? Nat Rev Rheumatol 2012; 8: 70-2.
2. Blagojevic M, Jinks C, Jeffery A, Jordan KP., Risk factors for onset of osteoarthritis of the knee in older adults: a systematic review and meta-analysis. Osteoarthritis Cartilage 2010; 18: 24-33.
3. Spector T., Risk factors for osteoarthritis: genetics. Osteoarthritis Cartilage 2004; 12: 39-44.
4. Valdes AM, Spector TD., The genetic epidemiology of osteoarthritis. Curr Opin Rheumatol 2010; 22: 139-43.
5. Gonzalez A., Osteoarthritis year 2013 in review: genetics and genomics. Osteoarthritis Cartilage 2013; 21: 1443-51.
6. Reynard LN, Loughlin J., The genetics and functional analysis of primary osteoarthritis susceptibility. Expert Rev Mol Med 2013; 15: e2.
7. Blanco FJ, Rego-Perez I., Is it time for epigenetics in osteoarthritis? [editorial]. Arthritis Rheumatol 2014; 66: 2324-7.
8. Dawson Mark A, Kouzarides T., Cancer epigenetics: from mechanism to therapy. Cell 2012; 150: 12-27.
9. Jones PA., The role of DNA methylation in mammalian epigenetics. Science 2001; 293: 1068-70.
10. Young DA., More evidence for a role of CpG methylation in the pathogenesis of osteoarthritis [editorial]. Arthritis Rheum 2013; 65: 555-8.
11. Hashimoto K, Oreffo RO, Gibson MB, Goldring MB, Roach HI., DNA demethylation at specific CpG sites in the IL1B promoter in response to inflammatory cytokines in human articular chondrocytes. Arthritis Rheum 2009; 60: 3303-13.
12. Roach HI, Yamada N, Cheung KS, Tilley S, Clarke NM, Oreffo RO, 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 2005; 52: 3110-24.
13. Cheung K, Hashimoto K, Yamada N, Roach H., Expression of ADAMTS-4 by chondrocytes in the surface zone of human osteoarthritic cartilage is regulated by epigenetic DNA de-methylation. Rheumatol Int 2009; 29: 525-34.
14. Hashimoto K, Otero M, Imagawa K, de Andres MC, Coico JM, Roach HI, et al., Regulated transcription of human matrix metalloproteinase 13 (MMP13) and interleukin-1 (IL1B) genes in chondrocytes depends on methylation of specific proximal promoter CpG sites. J Biol Chem 2013; 288: 10061-72.
15. Fernandez-Tajes J, Soto-Hermida A, Vazquez-Mosquera ME, 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 2014; 73: 668-77.
16. Rushton MD, Reynard LN, Barter MJ, Refaie R, Rankin KS, Young DA, et al., Characterization of the cartilage DNA methylome in knee and hip osteoarthritis: methylation profile of OA cartilage. Arthritis Rheumatol 2014; 66: 2450-60.
17. Jeffries MA, Donica M, Baker LW, Stevenson ME, Annan AC, Humphrey MB, et al., Genome-wide DNA methylation study identifies significant epigenomic changes in osteoarthritic cartilage. Arthritis Rheumatol 2014; 66: 2804-15.
18. Bhutani N, Burns DM, Blau HM., DNA demethylation dynamics. Cell 2011; 146: 866-72.
19. Kriaucionis S, Heintz N., The nuclear DNA base, 5-hydroxymethylcytosine is present in brain and enriched in Purkinje neurons. Science 2009; 324: 929-30.
20. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al., Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324: 930-5.
21. Bachman M, Uribe-Lewis S, Yang X, Williams M, Murrell A, Balasubramanian S., 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat Chem 2014; 6: 1049-55.
22. Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, et al., Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev 2011; 25: 679-84.
23. Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE,. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol 2011; 12: R54-62.
24. Hahn MA, Qiu R, Wu X, Li AX, Zhang H, Wang J, et al., Dynamics of 5-Hydroxymethylcytosine and chromatin marks in mammalian neurogenesis. Cell Rep 2013; 3: 291-300.
25. Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, et al., Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011; 473: 394-7.
26. Taylor SE, Smeriglio P, Dhulipala L, Rath M, Bhutani N., A global increase in 5-hydroxymethylcytosine levels marks osteoarthritic chondrocytes. Arthritis Rheumatol 2014; 66: 90-100.
27. Smith RL, Lindsey DP, Dhulipala L, Harris AH, Goodman SB, Maloney WJ,. Effects of intermittent hydrostatic pressure and BMP-2 on osteoarthritic human chondrocyte metabolism in vitro. J Orthop Res 2011; 29: 361-8.
28. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 2011; 29: 68-72.
29. Thomson JP, Hunter JM, Nestor CE, Dunican DS, Terranova R, Moggs JG, et al., Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques [published erratum appears in Nucleic Acids Res 2014;42:4142]. Nucleic Acids Res 2013; 41: e206.
30. Ivanov M, Kals M, Kacevska M, Barragan I, Kasuga K, Rane A, et al., Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function. Genome Biol 2013; 14: R83.
31. Li H, Durbin R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754-60.
32. Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ., diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One 2013; 8: e65598.
33. Shen L, Shao N, Liu X, Nestler E,. ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 2014; 15: 284.
34. Li C, Wong WH., Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A 2001; 98: 31-6.
35. Aigner T, Fundel K, Saas J, Gebhard PM, Haag J, Weiss T, et al., Large-scale gene expression profiling reveals major pathogenetic pathways of cartilage degeneration in osteoarthritis. Arthritis Rheum 2006; 54: 3533-44.
36. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, et al., Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011; 473: 398-402.
37. Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DB, et al., Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep 2014; 6: 231-44.
38. Chou CH, Lee CH, Lu LS, Song IW, Chuang HP, Kuo SY, et al., Direct assessment of articular cartilage and underlying subchondral bone reveals a progressive gene expression change in human osteoarthritic knees. Osteoarthritis Cartilage 2013; 21: 450-61.
39. Shen L, Shao N, Liu X, Nestler E., ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 2014; 15; 284.
40. Den Hollander W, Ramos YF, Bos SD, Bomer N, van der Breggen R, Lakenberg N, et al., Knee and hip articular cartilage have distinct epigenomic landscapes: implications for future cartilage regeneration approaches. Ann Rheum Dis 2014; 73: 2208-12.
41. Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A., The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010; 5: e8888.
42. Reynard LN, Bui C, Canty-Laird EG, Young DA, Loughlin J., Expression of the osteoarthritis-associated gene GDF5 is modulated epigenetically by DNA methylation. Hum Mol Genet 2011; 20: 3450-60.
43. Miller-Delaney SF, Lieberam I, Murphy P, Mitchell KJ., Plxdc2 is a mitogen for neural progenitors. PloS One 2011; 6: e14565.
44. Coser VM, Meyer C, Basegio R, Menezes J, Marschalek R, Pombo-de-Oliveira MS., Nebulette is the second member of the nebulin family fused to the MLL gene in infant leukemia. Cancer Genet Cytogenet 2010; 198: 151-4.
45. Sun W, Zang L, Shu Q, Li X., From development to diseases: the role of 5hmC in brain. Genomics 2014; 104: 347-51.
46. Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, et al., DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. Cell Rep 2014; 9: 1841-55.
47. Peffers MJ, Liu X, Clegg PD., Transcriptomic signatures in cartilage ageing. Arthritis Res Ther 2013; 15: R98.
48. Hosaka Y, Saito T, Sugita S, Hikata T, Kobayashi H, Fukai A, et al., Notch signaling in chondrocytes modulates endochondral ossification and osteoarthritis development. Proc Natl Acad Sci U S A 2013; 110: 1875-80.
49. Loughlin J, Dowling B, Chapman K, Marcelline L, Mustafa Z, Southam L, et al., Functional variants within the secreted frizzled-related protein 3 gene are associated with hip osteoarthritis in females. Proc Natl Acad Sci U S A 2004; 101: 9757-62.
50. Lin AC, Seeto BL, Bartoszko JM, Khoury MA, Whetstone H, Ho L, et al., Modulating hedgehog signaling can attenuate the severity of osteoarthritis. Nat Med 2009; 15: 1421-5.