Ahmed TA, Hincke MT: Strategies for articular cartilage lesion repair and functional restoration. Tissue Eng. 2010, 16 (3): 305-329. 10.1089/ten.teb.2009.0590.
Article
CAS
Google Scholar
Vinatier C, Bouffi C, Merceron C, Gordeladze J, Brondello JM, Jorgensen C, Weiss P, Guicheux J, Noel D: Cartilage tissue engineering: towards a biomaterial-assisted mesenchymal stem cell therapy. Curr Stem Cell Res Ther. 2009, 4 (4): 318-329. 10.2174/157488809789649205.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, Schreiber SL, Lander ES: Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005, 120 (2): 169-181. 10.1016/j.cell.2005.01.001.
Article
CAS
PubMed
Google Scholar
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O’Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007, 448 (7153): 553-560. 10.1038/nature06008.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B: Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 2010, 6 (5): 479-491. 10.1016/j.stem.2010.03.018.
Article
PubMed Central
CAS
PubMed
Google Scholar
Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA: Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2011, 44 (1): 23-31. 10.1038/ng.1009.
Article
PubMed Central
PubMed
Google Scholar
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA: A chromatin landmark and transcription initiation at most promoters in human cells. Cell. 2007, 130 (1): 77-88. 10.1016/j.cell.2007.05.042.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES: A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006, 125 (2): 315-326. 10.1016/j.cell.2006.02.041.
Article
CAS
PubMed
Google Scholar
Suganuma T, Workman JL: Signals and combinatorial functions of histone modifications. Annu Rev Biochem. 2011, 80: 473-499. 10.1146/annurev-biochem-061809-175347.
Article
CAS
PubMed
Google Scholar
Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, Lander ES, Rosen ED: Comparative epigenomic analysis of murine and human adipogenesis. Cell. 2010, 143 (1): 156-169. 10.1016/j.cell.2010.09.006.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sorensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P: Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage. Mol Biol Cell. 2010, 21 (12): 2066-2077. 10.1091/mbc.E10-01-0018.
Article
PubMed Central
PubMed
Google Scholar
Asp P, Blum R, Vethantham V, Parisi F, Micsinai M, Cheng J, Bowman C, Kluger Y, Dynlacht BD: Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci USA. 2011, 108 (22): E149-158. 10.1073/pnas.1102223108.
Article
PubMed Central
PubMed
Google Scholar
Lien WH, Guo X, Polak L, Lawton LN, Young RA, Zheng D, Fuchs E: Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell. 2011, 9 (3): 219-232. 10.1016/j.stem.2011.07.015.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cedar H, Bergman Y: Epigenetics of haematopoietic cell development. Nat Rev Immunol. 2011, 11 (7): 478-488. 10.1038/nri2991.
Article
CAS
PubMed
Google Scholar
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K: Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell. 2009, 4 (1): 80-93. 10.1016/j.stem.2008.11.011.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ: Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011, 44 (1): 17-28. 10.1016/j.molcel.2011.08.026.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ezura Y, Sekiya I, Koga H, Muneta T, Noda M: Methylation status of CpG islands in the promoter regions of signature genes during chondrogenesis of human synovium-derived mesenchymal stem cells. Arthritis Rheum. 2009, 60 (5): 1416-1426. 10.1002/art.24472.
Article
PubMed
Google Scholar
Furumatsu T, Asahara H: Histone acetylation influences the activity of Sox9-related transcriptional complex. Acta Med Okayama. 2011, 64 (6): 351-357.
Google Scholar
Zimmermann P, Boeuf S, Dickhut A, Boehmer S, Olek S, Richter W: Correlation of COL10A1 induction during chondrogenesis of mesenchymal stem cells with demethylation of two CpG sites in the COL10A1 promoter. Arthritis Rheum. 2008, 58 (9): 2743-2753. 10.1002/art.23736.
Article
PubMed
Google Scholar
Goldring MB, Tsuchimochi K, Ijiri K: The control of chondrogenesis. J Cell Biochem. 2006, 97 (1): 33-44. 10.1002/jcb.20652.
Article
CAS
PubMed
Google Scholar
Ichinose S, Yamagata K, Sekiya I, Muneta T, Tagami M: Detailed examination of cartilage formation and endochondral ossification using human mesenchymal stem cells. Clin Exp Pharmacol Physiol. 2005, 32 (7): 561-570. 10.1111/j.1440-1681.2005.04231.x.
Article
CAS
PubMed
Google Scholar
Lefebvre V, Smits P: Transcriptional control of chondrocyte fate and differentiation. Birth Defects Res C Embryo Today. 2005, 75 (3): 200-212. 10.1002/bdrc.20048.
Article
CAS
PubMed
Google Scholar
Lefebvre V, Behringer RR, de Crombrugghe B: L-Sox5, Sox6 and Sox9 control essential steps of the chondrocyte differentiation pathway. Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society. 2001, 9 (Suppl A): S69-75.
Article
PubMed
Google Scholar
Smits P, Li P, Mandel J, Zhang Z, Deng JM, Behringer RR, de Crombrugghe B, Lefebvre V: The transcription factors L-Sox5 and Sox6 are essential for cartilage formation. Dev Cell. 2001, 1 (2): 277-290. 10.1016/S1534-5807(01)00003-X.
Article
CAS
PubMed
Google Scholar
Ikeda T, Zhang J, Chano T, Mabuchi A, Fukuda A, Kawaguchi H, Nakamura K, Ikegawa S: Identification and characterization of the human long form of Sox5 (L-SOX5) gene. Gene. 2002, 298 (1): 59-68. 10.1016/S0378-1119(02)00927-7.
Article
CAS
PubMed
Google Scholar
Herlofsen SR, Kuchler AM, Melvik JE, Brinchmann JE: Chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells in self-gelling alginate discs reveals novel chondrogenic signature gene clusters. Tissue Eng Part A. 2011, 17 (7–8): 1003-1013.
Article
PubMed Central
CAS
PubMed
Google Scholar
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B: Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009, 459 (7243): 108-112. 10.1038/nature07829.
Article
PubMed Central
CAS
PubMed
Google Scholar
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007, 39 (3): 311-318. 10.1038/ng1966.
Article
CAS
PubMed
Google Scholar
Tew SR, Clegg PD, Brew CJ, Redmond CM, Hardingham TE: SOX9 transduction of a human chondrocytic cell line identifies novel genes regulated in primary human chondrocytes and in osteoarthritis. Arthritis Res Ther. 2007, 9 (5): R107-10.1186/ar2311.
Article
PubMed Central
PubMed
Google Scholar
Kerney R, Hall BK, Hanken J: Regulatory elements of Xenopus col2a1 drive cartilaginous gene expression in transgenic frogs. Int J Dev Biol. 2010, 54 (1): 141-150. 10.1387/ijdb.092848rk.
Article
CAS
PubMed
Google Scholar
Lefebvre V, Huang W, Harley VR, Goodfellow PN, de Crombrugghe B: SOX9 is a potent activator of the chondrocyte-specific enhancer of the pro alpha1(II) collagen gene. Mol Cell Biol. 1997, 17 (4): 2336-2346.
Article
PubMed Central
CAS
PubMed
Google Scholar
Oh CD, Maity SN, Lu JF, Zhang J, Liang S, Coustry F, de Crombrugghe B, Yasuda H: Identification of SOX9 interaction sites in the genome of chondrocytes. PLoS One. 2010, 5 (4): e10113-10.1371/journal.pone.0010113.
Article
PubMed Central
PubMed
Google Scholar
Zhou G, Lefebvre V, Zhang Z, Eberspaecher H, de Crombrugghe B: Three high mobility group-like sequences within a 48-base pair enhancer of the Col2a1 gene are required for cartilage-specific expression in vivo. J Biol Chem. 1998, 273 (24): 14989-14997. 10.1074/jbc.273.24.14989.
Article
CAS
PubMed
Google Scholar
Park JS, Yang HN, Woo DG, Jeon SY, Do HJ, Lim HY, Kim JH, Park KH: Chondrogenesis of human mesenchymal stem cells mediated by the combination of SOX trio SOX5, 6, and 9 genes complexed with PEI-modified PLGA nanoparticles. Biomaterials. 2011, 32 (14): 3679-3688. 10.1016/j.biomaterials.2011.01.063.
Article
CAS
PubMed
Google Scholar
Amarilio R, Viukov SV, Sharir A, Eshkar-Oren I, Johnson RS, Zelzer E: HIF1alpha regulation of Sox9 is necessary to maintain differentiation of hypoxic prechondrogenic cells during early skeletogenesis. Development. 2007, 134 (21): 3917-3928. 10.1242/dev.008441.
Article
CAS
PubMed
Google Scholar
Greenwel P, Inagaki Y, Hu W, Walsh M, Ramirez F: Sp1 is required for the early response of alpha2(I) collagen to transforming growth factor-beta1. J Biol Chem. 1997, 272 (32): 19738-19745. 10.1074/jbc.272.32.19738.
Article
CAS
PubMed
Google Scholar
Iwamoto M, Higuchi Y, Enomoto-Iwamoto M, Kurisu K, Koyama E, Yeh H, Rosenbloom J, Pacifici M: The role of ERG (ets related gene) in cartilage development. Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society. 2001, 9 (Suppl A): S41-47.
Article
PubMed
Google Scholar
Nakada C, Iida A, Tabata Y, Watanabe S: Forkhead transcription factor foxe1 regulates chondrogenesis in zebrafish. J Exp Zool. 2009, 312 (8): 827-840.
Article
Google Scholar
Boquest AC, Shahdadfar A, Fronsdal K, Sigurjonsson O, Tunheim SH, Collas P, Brinchmann JE: Isolation and transcription profiling of purified uncultured human stromal stem cells: alteration of gene expression after in vitro cell culture. Mol Biol Cell. 2005, 16 (3): 1131-1141. 10.1091/mbc.E04-10-0949.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nombela-Arrieta C, Ritz J, Silberstein LE: The elusive nature and function of mesenchymal stem cells. Nature reviews. 2011, 12 (2): 126-131. 10.1038/nrm3049.
Article
PubMed Central
CAS
PubMed
Google Scholar
Weake VM, Workman JL: Inducible gene expression: diverse regulatory mechanisms. Nat Rev Genet. 2010, 11 (6): 426-437. 10.1038/nrg2781.
Article
CAS
PubMed
Google Scholar
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Ostrup O, Winata C, Mathavan S, Muller F, Alestrom P, Collas P: Prepatterning of developmental gene expression by modified histones before zygotic genome activation. Dev Cell. 2011, 21 (6): 993-1004. 10.1016/j.devcel.2011.10.008.
Article
CAS
PubMed
Google Scholar
Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G: Genome regulation by polycomb and trithorax proteins. Cell. 2007, 128 (4): 735-745. 10.1016/j.cell.2007.02.009.
Article
CAS
PubMed
Google Scholar
Pirngruber J, Shchebet A, Johnsen SA: Insights into the function of the human P-TEFb component CDK9 in the regulation of chromatin modifications and co-transcriptional mRNA processing. Cell cycle (Georgetown, Tex). 2009, 8 (22): 3636-3642. 10.4161/cc.8.22.9890.
Article
CAS
Google Scholar
Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van Schaik FM, Varier RA, Baltissen MP, Stunnenberg HG, Mann M, Timmers HT: Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell. 2007, 131 (1): 58-69. 10.1016/j.cell.2007.08.016.
Article
CAS
PubMed
Google Scholar
Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M: Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010, 142 (6): 967-980. 10.1016/j.cell.2010.08.020.
Article
CAS
PubMed
Google Scholar
Yun M, Wu J, Workman JL, Li B: Readers of histone modifications. Cell Res. 2011, 21 (4): 564-578. 10.1038/cr.2011.42.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yoh SM, Lucas JS, Jones KA: The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes Dev. 2008, 22 (24): 3422-3434. 10.1101/gad.1720008.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dysvik B, Jonassen I: J-Express: exploring gene expression data using Java. Bioinformatics (Oxford, England). 2001, 17 (4): 369-370. 10.1093/bioinformatics/17.4.369.
Article
CAS
Google Scholar
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J: Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet. 2009, 41 (3): 376-381. 10.1038/ng.322.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010, 7 (2): 133-136. 10.1038/nmeth.1414.
Article
PubMed Central
CAS
PubMed
Google Scholar
Murdoch AD, Grady LM, Ablett MP, Katopodi T, Meadows RS, Hardingham TE: Chondrogenic differentiation of human bone marrow stem cells in transwell cultures: generation of scaffold-free cartilage. Stem Cells. 2007, 25 (11): 2786-2796. 10.1634/stemcells.2007-0374.
Article
CAS
PubMed
Google Scholar