Histone chip-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works

GREAT improves functional interpretation of cis-regulatory regions

McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502 · see citing works

Osteoarthritis: A disease of the joint as an organ

Loeser, R. F., Goldring, S. R., Scanzello, C. R., & Goldring, M. B. (2012) · Arthritis & Rheumatism · doi:10.1002/art.34453 · Cited by 3,129 · see citing works

ChromHMM: automating chromatin-state discovery and characterization

Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works

In VitroChondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells

Johnstone, B., Hering, T. M., Caplan, A. I., Goldberg, V. M., & Yoo, J. U. (1998) · Experimental Cell Research · doi:10.1006/excr.1997.3858 · Cited by 2,381 · see citing works

Linking DNA methylation and histone modification: patterns and paradigms

Cedar, H., & Bergman, Y. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2540 · Cited by 2,267 · see citing works

MEME-ChIP: motif analysis of large DNA datasets

Machanick, P., & Bailey, T. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr189 · Cited by 1,815 · see citing works

Identifying ChIP-seq enrichment using MACS

Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.101 · Cited by 1,805 · see citing works

SOX9 Is a Potent Activator of the Chondrocyte-Specific Enhancer of the Proα1(II) Collagen Gene

Lefebvre, V., Huang, W., Harley, V. R., Goodfellow, P. N., & Crombrugghe, B. D. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.4.2336 · Cited by 1,077 · see citing works

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.037 · Cited by 1,046 · see citing works

Endochondral ossification: How cartilage is converted into bone in the developing skeleton

Mackie, E. J., Ahmed, Y. A., Tatarczuch, L., Chen, K.-S., & Mirams, M. (2007) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2007.06.009 · Cited by 1,024 · see citing works

The selection and function of cell type-specific enhancers

Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010 · see citing works

SOX9 directly regulates the type-ll collagen gene

Bell, D. M., Leung, K. K. H., Wheatley, S. C., Ng, L. J., Zhou, S. X., Ling, K., Sham, M. H., Koopman, P. A., Tam, P., & Cheah, K. S. E. (1997) · Nature Genetics · doi:10.1038/ng0697-174 · Cited by 933 · see citing works

From head to toes: the multiple facets of Sox proteins

Wegner, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.6.1409 · Cited by 890 · see citing works

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

Shen, L., Shao, N., Liu, X., & Nestler, E. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-284 · Cited by 852 · see citing works

Chromatin Domains: The Unit of Chromosome Organization

Dixon, J. R., Gorkin, D. U., & Ren, B. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.018 · Cited by 811 · see citing works

Chondrocyte hypertrophy and osteoarthritis: role in initiation and progression of cartilage degeneration?

van der Kraan, P. M., & van den Berg, W. B. (2011) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2011.12.003 · Cited by 661 · see citing works

MicroRNA-140 plays dual roles in both cartilage development and homeostasis

Miyaki, S., Sato, T., Inoue, A., Otsuki, S., Ito, Y., Yokoyama, S., Kato, Y., Takemoto, F., Nakasa, T., Yamashita, S., et al. (2010) · Genes & Development · doi:10.1101/gad.1915510 · Cited by 660 · see citing works

Functional characterization of hypertrophy in chondrogenesis of human mesenchymal stem cells

Mueller, M. B., & Tuan, R. S. (2008) · Arthritis & Rheumatism · doi:10.1002/art.23370 · Cited by 490 · see citing works

Signalling mediated by the endoplasmic reticulum stress transducer OASIS is involved in bone formation

Murakami, T., Saito, A., Hino, S., Kondo, S., Kanemoto, S., Chihara, K., Sekiya, H., Tsumagari, K., Ochiai, K., Yoshinaga, K., et al. (2009) · Nature Cell Biology · doi:10.1038/ncb1963 · Cited by 410 · see citing works

DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells

Bock, C., Beerman, I., Lien, W., Smith, Z. D., Gu, H., Boyle, P., Gnirke, A., Fuchs, E. V., Rossi, D. J., & Meissner, A. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.019 · Cited by 378 · see citing works

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis

Liu, C.-F., & Lefebvre, V. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv688 · Cited by 287 · see citing works

Control of chondrogenesis by the transcription factor Sox9

Akiyama, H. (2008) · Modern Rheumatology · doi:10.1007/s10165-008-0048-x · Cited by 286 · see citing works

Multigenerational epigenetic adaptation of the hepatic wound-healing response

Zeybel, M., Hardy, T., Wong, Y. K., Mathers, J. C., Fox, C. R., Gackowska, A., Oakley, F., Burt, A. D., Wilson, C. L., Anstee, Q. M., et al. (2012) · Nature Medicine · doi:10.1038/nm.2893 · Cited by 279 · see citing works

ASSEMBLY OF VARIANT HISTONES INTO CHROMATIN

Henikoff, S., & Ahmad, K. (2005) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.21.012704.133518 · Cited by 278 · see citing works

MicroRNA-145 Regulates Chondrogenic Differentiation of Mesenchymal Stem Cells by Targeting Sox9

Yang, B., Guo, H., Zhang, Y., Chen, L., Ying, D., & Dong, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021679 · Cited by 268 · see citing works

Chondrogenic Differentiation of Human Bone Marrow Stem Cells in Transwell Cultures: Generation of Scaffold-Free Cartilage

Murdoch, A. D., Grady, L., Ablett, M. P., Katopodi, T., Meadows, R. S., & Hardingham, T. (2007) · Stem Cells · doi:10.1634/stemcells.2007-0374 · Cited by 258 · see citing works

Functional Analysis of Promoter CPG-Methylation using a CpG-Free Luciferase Reporter Vector

Klug, M., & Rehli, M. (2006) · Epigenetics · doi:10.4161/epi.1.3.3327 · Cited by 249 · see citing works

Identification of a Prg4 ‐Expressing Articular Cartilage Progenitor Cell Population in Mice

Kozhemyakina, E. A., Zhang, M., Ionescu, A. M., Ayturk, U. M., Ono, N., Kobayashi, A., Kronenberg, H. M., Warman, M. L., & Lassar, A. B. (2015) · Arthritis & Rheumatology · doi:10.1002/art.39030 · Cited by 247 · see citing works

Chondrogenic differentiation of human mesenchymal stem cells: a comparison between micromass and pellet culture systems

Zhang, L., Su, P., Xu, C., Yang, J., Yu, W., & Huang, D. (2010) · Biotechnology Letters · doi:10.1007/s10529-010-0293-x · Cited by 243 · see citing works

Motif-based analysis of large nucleotide data sets using MEME-ChIP

Ma, W., Noble, W. S., & Bailey, T. L. (2014) · Nature Protocols · doi:10.1038/nprot.2014.083 · Cited by 237 · see citing works

Collagen type II suppresses articular chondrocyte hypertrophy and osteoarthritis progression by promoting integrin β1−SMAD1 interaction

Lian, C., Wang, X., Qiu, X., Wu, Z., Gao, B., Liu, L., Liang, G., Zhou, H., Yang, X., Peng, Y., et al. (2019) · Bone Research · doi:10.1038/s41413-019-0046-y · Cited by 234 · see citing works

Cooperation Between TGF-β and Wnt Pathways During Chondrocyte and Adipocyte Differentiation of Human Marrow Stromal Cells

Zhou, S., Eid, K., & Glowacki, J. (2004) · Journal of Bone and Mineral Research · doi:10.1359/jbmr.0301239 · Cited by 226 · see citing works

SOX9 Governs Differentiation Stage-Specific Gene Expression in Growth Plate Chondrocytes via Direct Concomitant Transactivation and Repression

Leung, V., Gao, B., Leung, K. K. H., Melhado, I. G., Wynn, S. L., Au, T. Y. K., Dung, N. W. F., Lau, J. Y. B., Mak, A. C. Y., Chan, D. T.-M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002356 · Cited by 219 · see citing works

Increased type II collagen degradation and very early focal cartilage degeneration is associated with upregulation of chondrocyte differentiation related genes in early human articular cartilage lesions.

Tchetina, E. V., Squires, G. R., & Poole, A. R. (2005) · PubMed · Cited by 213 · see citing works

Hypertrophy in Mesenchymal Stem Cell Chondrogenesis: Effect of TGF-β Isoforms and Chondrogenic Conditioning

Mueller, M. B., Fischer, M., Zellner, J., Berner, A., Dienstknecht, T., Prantl, L., Kujat, R., Nerlich, M. L., Tuan, R. S., & Angele, P. (2010) · Cells Tissues Organs · doi:10.1159/000313399 · Cited by 211 · see citing works

Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer

Heyn, H., Vidal, E., Ferreira, H. J., Vizoso, M., Sayols, S., Gómez, A., Morán, S., Boqué-Sastre, R., Guil, S., Martínez‐Cardús, A., et al. (2016) · Genome biology · doi:10.1186/s13059-016-0879-2 · Cited by 209 · see citing works

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

Cotney, J. L., Leng, J., Yin, J., Reilly, S. K., DeMare, L. E., Emera, D., Ayoub, A. E., RAKIC, P. T., & Noonan, J. P. (2013) · Cell · doi:10.1016/j.cell.2013.05.056 · Cited by 208 · see citing works

DNA methylation is required for the control of stem cell differentiation in the small intestinePreprint

Sheaffer, K. L., Kim, R., Aoki, R., Elliott, E. N., Schug, J., Burger, L., Schübeler, D., & Kaestner, K. H. (2014) · Genes & Development · doi:10.1101/gad.230318.113 · Cited by 205 · see citing works

Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations

Meyer, J. (1997) · Human Molecular Genetics · doi:10.1093/hmg/6.1.91 · Cited by 204 · see citing works

Transcription factors mediate long-range enhancer–promoter interactions

Nolis, I. K., McKay, D. J., Mantouvalou, E., Lomvardas, S., Merika, M., & Thanos, D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902454106 · Cited by 191 · see citing works

Distinct Transcriptional Programs Underlie Sox9 Regulation of the Mammalian Chondrocyte

Ohba, S., He, X., Hojo, H., & McMahon, A. P. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.06.013 · Cited by 179 · see citing works

DNA methylation in human epigenomes depends on local topology of CpG sites

Lövkvist, C., Dodd, I. B., Sneppen, K., & Haerter, J. O. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw124 · Cited by 178 · see citing works

Recent Progress in Cartilage Tissue Engineering—Our Experience and Future Directions

Liu, Y., Zhou, G., & Cao, Y. (2017) · Engineering · doi:10.1016/j.eng.2017.01.010 · Cited by 165 · see citing works

Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia

Wunderle, V. M., Critcher, R., Hastie, N. D., Goodfellow, P. N., & Schedl, A. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.18.10649 · Cited by 159 · see citing works

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

Smith, E. M., Lajoie, B. R., Jain, G., & Dekker, J. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.12.002 · Cited by 142 · see citing works

MiR-140 is co-expressed withWwp2-Ctranscript and activated by Sox9 to targetSp1in maintaining the chondrocyte proliferation

Yang, J., Qin, S., Yi, C., Ma, G., Huang, Z., Zhou, W., Xiong, Y., Zhu, X., Wang, Y., He, L., et al. (2011) · FEBS Letters · doi:10.1016/j.febslet.2011.08.013 · Cited by 135 · see citing works

An 18-Base-Pair Sequence in the Mouse Proα1(II) Collagen Gene Is Sufficient for Expression in Cartilage and Binds Nuclear Proteins That Are Selectively Expressed in Chondrocytes

Lefebvre, V., Zhou, G. D., Mukhopadhyay, K., Smith, C. N., Zhang, Z., Eberspaecher, H., Zhou, X., Sinha, S., Maity, S. N., & Crombrugghe, B. D. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.8.4512 · Cited by 131 · see citing works

Deficiency for the ER-stress transducer OASIS causes severe recessive osteogenesis imperfecta in humans

Symoens, S., Malfait, F., D’hondt, S., Callewaert, B. L., Dheedene, A., Steyaert, W., Bächinger, H. P., Paepe, A. D., Kayserili, H., & Coucke, P. J. (2013) · Orphanet Journal of Rare Diseases · doi:10.1186/1750-1172-8-154 · Cited by 126 · see citing works

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

Sharifi‐Zarchi, A., Daniela Gerovska, D., Adachi, K., Totonchi, M., Pezeshk, H., Taft, R. J., Schöler, H. R., Chitsaz, H., Sadeghi, M., Baharvand, H., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-4353-7 · Cited by 123 · see citing works

Enhancer methylation dynamics contribute to cancer plasticity and patient mortalityPreprint

Bell, R. E., Golan, T., Sheinboim, D., Malcov, H., Amar, D., Salamon, A., Liron, T., Gelfman, S., Gabet, Y., Ron Shamir, A., et al. (2016) · Genome Research · doi:10.1101/gr.197194.115 · Cited by 116 · see citing works

Wwp2 maintains cartilage homeostasis through regulation of Adamts5

Mokuda, S., Nakamichi, R., Matsuzaki, T., Ito, Y., Sato, T., Miyata, K., Inui, M., Olmer, M., Sugiyama, E., Lotz, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10177-1 · Cited by 111 · see citing works

Genome-Wide MicroRNA and Gene Analysis of Mesenchymal Stem Cell Chondrogenesis Identifies an Essential Role and Multiple Targets for miR-140-5p

Barter, M. J., Tselepi, M., Gómez, R., Woods Jon, S., Wang, H., Smith, G. R., Shanley, D. P., Clark, I. M., & Young, D. A. (2015) · Stem Cells · doi:10.1002/stem.2093 · Cited by 102 · see citing works

Identification of SOX9 Interaction Sites in the Genome of Chondrocytes

Oh, C., Maity, S. N., Lu, J.-F., Zhang, J., Liang, S., Coustry, F., Crombrugghe, B. D., & Yasuda, H. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010113 · Cited by 99 · see citing works

Structural and Functional Characterization of the Mouse Sox9 Promoter: Implications for Campomelic Dysplasia

Kanai, Y., & Koopman, P. A. (1999) · Human Molecular Genetics · doi:10.1093/hmg/8.4.691 · Cited by 99 · see citing works

Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk

Capellini, T. D., Chen, H., Cao, J., Doxey, A. C., Kiapour, A. M., Schoor, M., & Kingsley, D. M. (2017) · Nature Genetics · doi:10.1038/ng.3911 · Cited by 96 · see citing works

E74-like Factor 3 (ELF3) Impacts on Matrix Metalloproteinase 13 (MMP13) Transcriptional Control in Articular Chondrocytes under Proinflammatory Stress

Otero, M., Plumb, D. A., Tsuchimochi, K., Dragomir, C. L., Hashimoto, K., Peng, H., Olivotto, E., Bevilacqua, M., Tan, L., Yang, Z., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.265744 · Cited by 94 · see citing works

Positional specificity of different transcription factor classes within enhancers

Grossman, S. R., Engreitz, J., Ray, J. P., Nguyen, T. H., Hacohen, N., & Lander, E. S. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1804663115 · Cited by 88 · see citing works

The long non-coding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells

Barter, M. J., Gómez, R., Hyatt, S., Cheung, K., Skelton, A. J., Xu, Y., Clark, I. M., & Young, D. A. (2017) · Development · doi:10.1242/dev.152504 · Cited by 80 · see citing works

Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells

Herlofsen, S. R., Bryne, J. C., Høiby, T., Wang, L., Issner, R., Zhang, X., Coyne, M. J., Boyle, P., Gu, H., Meza‐Zepeda, L. A., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-105 · Cited by 79 · see citing works

Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage

Álvarez-García, Ó., Fisch, K. M., Wineinger, N. E., Akagi, R., Saito, M., Sasho, T., Su, A. I., & Lotz, M. (2016) · Arthritis & Rheumatology · doi:10.1002/art.39643 · Cited by 75 · see citing works

SOX9 transduction of a human chondrocytic cell line identifies novel genes regulated in primary human chondrocytes and in osteoarthritis

Tew, S. R., Clegg, P., Brew, C. J., Redmond, C. M., & Hardingham, T. (2007) · Arthritis Research & Therapy · doi:10.1186/ar2311 · Cited by 74 · see citing works

SOX9 is dispensable for the initiation of epigenetic remodeling and the activation of marker genes at the onset of chondrogenesis

Liu, C.-F., Angelozzi, M., Haseeb, A., & Lefebvre, V. (2018) · Development · doi:10.1242/dev.164459 · Cited by 73 · see citing works

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

Sebastián, Á., & Contreras‐Moreira, B. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt663 · Cited by 73 · see citing works

Cartilage Repair With Autologous Bone Marrow Mesenchymal Stem Cell Transplantation

Yamasaki, S., Mera, H., Itokazu, M., Hashimoto, Y., & Wakitani, S. (2014) · Cartilage · doi:10.1177/1947603514534681 · Cited by 73 · see citing works

Monoallelic and biallelic CREB3L1 variant causes mild and severe osteogenesis imperfecta, respectively

Keller, R. B., Tran, T., Pyott, S. M., Pepin, M. G., Savarirayan, R., McGillivray, G., Nickerson, D. A., Bamshad, M. J., & Byers, P. H. (2017) · Genetics in Medicine · doi:10.1038/gim.2017.115 · Cited by 71 · see citing works

Runx2 contributes to murine Col10a1 gene regulation through direct interaction with its cis-enhancer

Li, F., Lu, Y., Ding, M., Napierala, D., Abbassi, S., Chen, Y., Duan, X., Wang, S., Lee, B., & Zheng, Q. (2011) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.504 · Cited by 71 · see citing works

A Comparison of Three-Dimensional Culture Systems to Evaluate In Vitro Chondrogenesis of Equine Bone Marrow-Derived Mesenchymal Stem Cells

Watts, A. E., Ackerman-Yost, J. C., & Nixon, A. J. (2013) · Tissue Engineering Part A · doi:10.1089/ten.tea.2012.0479 · Cited by 71 · see citing works

DNA methylation reprogramming of functional elements during mammalian embryonic development

Li, C., Fan, Y., Li, G., Xu, X., Duan, J., Li, R., Kang, X., Ma, X., Chen, X., Ke, Y., et al. (2018) · Cell Discovery · doi:10.1038/s41421-018-0039-9 · Cited by 70 · see citing works

High‐depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis

Huynh, N. P. T., Zhang, B., & Guilak, F. (2018) · The FASEB Journal · doi:10.1096/fj.201800534r · Cited by 69 · see citing works

An epigenetic switch regulatesde novoDNA methylation at a subset of pluripotency gene enhancers during embryonic stem cell differentiation

Petell, C. J., AlAbdi, L., He, M., Miguel, P. S., Rose, R., & Gowher, H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw426 · Cited by 64 · see citing works

Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

Liu, Y., Chang, J.-C., Hon, C.-C., Fukui, N., Tanaka, N., Zhang, Z., Lee, M. T. M., & Minoda, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-33779-z · Cited by 63 · see citing works

Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes

Ferguson, G. B., Handel, B. V., Bay, M., Fiziev, P. P., Org, T., Lee, S., Shkhyan, R., Banks, N. W., Scheinberg, M., Wu, L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05573-y · Cited by 63 · see citing works

AP-1 family members act with Sox9 to promote chondrocyte hypertrophy

He, X., Ohba, S., Hojo, H., & McMahon, A. P. (2016) · Development · doi:10.1242/dev.134502 · Cited by 61 · see citing works

MicroRNA-30a promotes chondrogenic differentiation of mesenchymal stem cells through inhibiting Delta-like 4 expression

Tian, Y. E., Guo, R., Shi, B., Chen, L., Yang, L., & Fu, Q. (2016) · Life Sciences · doi:10.1016/j.lfs.2016.02.031 · Cited by 58 · see citing works

Notch1 signaling regulates chondrogenic lineage determination through Sox9 activation

Haller, R., Schwanbeck, R., Martini, S., Bernoth, K., Kramer, J., Just, U., & Rohwedel, J. (2011) · Cell Death and Differentiation · doi:10.1038/cdd.2011.114 · Cited by 53 · see citing works

Genome-wide DNA methylation profile implicates potential cartilage regeneration at the late stage of knee osteoarthritis

Zhang, Y., Fukui, N., Yahata, M., Katsuragawa, Y., Tashiro, T., Ikegawa, S., & Lee, M. T. M. (2015) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2015.12.013 · Cited by 52 · see citing works

Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux

Palstra, R.-J. T. S., & Grosveld, F. G. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00195 · Cited by 50 · see citing works

The development of a mature collagen network in cartilage from human bone marrow stem cells in Transwell culture

Murdoch, A. D., Hardingham, T., Eyre, D. R., & Fernandes, R. J. (2015) · Matrix Biology · doi:10.1016/j.matbio.2015.10.003 · Cited by 47 · see citing works

Making sense of chromatin states

Baker, M. (2011) · Nature Methods · doi:10.1038/nmeth.1673 · Cited by 43 · see citing works

A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-dependent Enhancer in Intron 6

Yasuda, H., Oh, C., Chen, D., Crombrugghe, B. D., & Kim, J. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.758425 · Cited by 43 · see citing works

Epigenetic regulation in chondrogenesis.

Furumatsu, T., & Ozaki, T. (2010) · PubMed · doi:10.18926/amo/40007 · Cited by 43 · see citing works

ELF3 modulates type II collagen gene (COL2A1) transcription in chondrocytes by inhibiting SOX9-CBP/p300-driven histone acetyltransferase activity

Otero, M., Peng, H., Hachem, K. E., Culley, K. L., Wondimu, E. B., Quinn, J., Asahara, H., Tsuchimochi, K., Hashimoto, K., & Goldring, M. B. (2016) · Connective Tissue Research · doi:10.1080/03008207.2016.1200566 · Cited by 43 · see citing works

Identification of molecular markers for articular cartilage

Hissnauer, T. N., Baranowsky, A., Pestka, J. M., Streichert, T., Wiegandt, K., Goepfert, C., Beil, F. T., Albers, J., Schulze, J., Ueblacker, P., et al. (2010) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2010.10.002 · Cited by 43 · see citing works

Low-density lipoprotein receptor–related protein 5 governs Wnt-mediated osteoarthritic cartilage destruction

Shin, Y., Huh, Y. H., Kim, K., Kim, S., Park, K. H., Koh, J., Chun, J., & Ryu, J. (2014) · Arthritis Research & Therapy · doi:10.1186/ar4466 · Cited by 38 · see citing works

Cancer-specific changes in DNA methylation reveal aberrant silencing and activation of enhancers in leukemia

Qu, Y., Siggens, L., Cordeddu, L., Gaidzik, V. I., Karlsson, K., Bullinger, L., Döhner, K., Ekwall, K., Lehmann, S., & Lennartsson, A. (2016) · Blood · doi:10.1182/blood-2016-07-726877 · Cited by 37 · see citing works

HES factors regulate specific aspects of chondrogenesis and chondrocyte hypertrophy during cartilage development

Rutkowski, T. P., Kohn, A., Sharma, D., Ren, Y., Mirando, A. J., & Hilton, M. J. (2016) · Journal of Cell Science · doi:10.1242/jcs.181271 · Cited by 36 · see citing works

Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements

Pasumarthy, K. K., Jayavelu, N. D., Kilpinen, L., Andrus, C. R., Battle, S. L., Korhonen, M. O., Lehenkari, P. P., Lund, R., Laitinen, S., & Hawkins, R. D. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.07.018 · Cited by 35 · see citing works

Probing transcription factor combinatorics in different promoter classes and in enhancers

Vandel, J., Cassan, O., Lèbre, S., Lecellier, C., & Bréhélin, L. (2019) · BMC Genomics · doi:10.1186/s12864-018-5408-0 · Cited by 35 · see citing works

Elf3 Contributes to Cartilage Degradation in vivo in a Surgical Model of Post-Traumatic Osteoarthritis

Wondimu, E. B., Culley, K. L., Quinn, J., Chang, J., Dragomir, C. L., Plumb, D. A., Goldring, M. B., & Otero, M. (2018) · Scientific Reports · doi:10.1038/s41598-018-24695-3 · Cited by 33 · see citing works

Gene expression analysis of human otosclerotic stapedial footplates

Ealy, M., Chen, W., Ryu, G., Yoon, J., Welling, D. B., Hansen, M. R., Madan, A., & Smith, R. J. (2008) · Hearing Research · doi:10.1016/j.heares.2008.03.001 · Cited by 32 · see citing works

Methods for Producing Scaffold-Free Engineered Cartilage Sheets from Auricular and Articular Chondrocyte Cell Sources and Attachment to Porous Tantalum

Whitney, G. A., Mera, H., Weidenbecher, M. S., Awadallah, A., Mansour, J. M., & Dennis, J. E. (2012) · BioResearch open access · doi:10.1089/biores.2012.0231 · Cited by 32 · see citing works

SOX9 has both conserved and novel roles in marsupial sexual differentiation

Pask, A. J., Harry, J. L., Graves, J. A. M., O'Neill, R. J. W., Layfield, S. L., Shaw, G., & Renfree, M. B. (2002) · genesis · doi:10.1002/gene.10096 · Cited by 30 · see citing works

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Barter, M. J., Bui, C., Cheung, K., Falk, J., Gómez, R., Skelton, A. J., Elliott, H. R., Reynard, L. N., & Young, D. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-58093-5 · Cited by 27 · see citing works

Post-transcriptional gene regulation following exposure of osteoarthritic human articular chondrocytes to hyperosmotic conditions

Tew, S. R., Vasieva, O., Peffers, M. J., & Clegg, P. (2011) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2011.04.015 · Cited by 27 · see citing works

Differential tissue specific, temporal and spatial expression patterns of the Aggrecan gene is modulated by independent enhancer elements

Li, I. M. H., Liu, K., Neal, A., Clegg, P., Val, S. D., & Bou-Gharios, G. (2018) · Scientific Reports · doi:10.1038/s41598-018-19186-4 · Cited by 22 · see citing works

Further complexity of the human SOX gene family revealed by the combined use of highly degenerate primers and nested PCR

Crémazy, F. G. E., Soullier, S., Berta, P., & Jay, P. (1998) · FEBS Letters · doi:10.1016/s0014-5793(98)01294-0 · Cited by 22 · see citing works

Expression of TLE3 by bone marrow stromal cells is regulated by canonical Wnt signaling

Kokabu, S., Sato, T., Ohte, S., Enoki, Y., Okubo, M., Hayashi, N., Nojima, J., Tsukamoto, S., Fukushima, Y., Sakata, Y., et al. (2014) · FEBS Letters · doi:10.1016/j.febslet.2013.12.031 · Cited by 21 · see citing works

The first family with adult osteogenesis imperfecta caused by a novel homozygous mutation in CREB3L1

Cayami, F. K., Maugeri, A., Treurniet, S., Setijowati, E. D., Teunissen, B. P., Eekhoff, E. M. W., Pals, G., Faradz, S. M., & Micha, D. (2019) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.823 · Cited by 20 · see citing works

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

Lee, W. J., Chatterjee, S., Yap, S. P., Lim, S. L., Xing, X., Kraus, P., Sun, W., Hu, T. X., Vijayakumar, S., Chan, H. Y., et al. (2017) · BioMed Research International · doi:10.1155/2017/8932583 · Cited by 16 · see citing works

Functional Characterization of the Osteoarthritis Susceptibility Mapping to CHST11—A Bioinformatics and Molecular Study

Reynard, L. N., Ratnayake, M., Santibanez‐Koref, M., & Loughlin, J. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0159024 · Cited by 14 · see citing works

Epigenetic regulation of chondrocyte differentiation

Hata, K. (2015) · Japanese Dental Science Review · doi:10.1016/j.jdsr.2015.05.001 · Cited by 12 · see citing works

How does hip osteoarthritis differ from knee osteoarthritis?

Hall, M., van der Esch, M., Hinman, R. S., Peat, G., de Zwart, A. H., Quicke, J. G., Runhaar, J., Knoop, J., van der Leeden, M., de Rooij, M., et al. (2021) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2021.09.010 · Cited by 210 · see citing works

Mesenchymal stem cells under epigenetic control – the role of epigenetic machinery in fate decision and functional properties

Walewska, A., Janucik, A., Tynecka, M., Moniuszko, M., & Eljaszewicz, A. (2023) · Cell Death and Disease · doi:10.1038/s41419-023-06239-4 · Cited by 63 · see citing works

STAT3 promotes a youthful epigenetic state in articular chondrocytes

Sarkar, A., Liu, N. Q., Magallanes, J., Tassey, J., Lee, S., Shkhyan, R., Lee, Y., Lu, J., Ouyang, Y., Tang, H., et al. (2023) · Aging Cell · doi:10.1111/acel.13773 · Cited by 42 · see citing works

Epigenetic therapy targeting bone marrow mesenchymal stem cells for age-related bone diseases

Zhao, Y., He, J., Qiu, T., Zhang, H., Liao, L., & Su, X. (2022) · Stem Cell Research & Therapy · doi:10.1186/s13287-022-02852-w · Cited by 39 · see citing works

SOX9 reprograms endothelial cells by altering the chromatin landscape

Fuglerud, B. M., Drissler, S., Lotto, J., Stephan, T. L., Thakur, A., Cullum, R., & Hoodless, P. A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac652 · Cited by 35 · see citing works

Epigenetic Regulators of Mesenchymal Stem/Stromal Cell Lineage Determination

Cakouros, D., & Gronthos, S. (2020) · Current Osteoporosis Reports · doi:10.1007/s11914-020-00616-0 · Cited by 35 · see citing works

Emerging RUNX2-Mediated Gene Regulatory Mechanisms Consisting of Multi-Layered Regulatory Networks in Skeletal Development

Hojo, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032979 · Cited by 32 · see citing works

Histone Modifications and Chondrocyte Fate: Regulation and Therapeutic Implications

Wan, C., Zhang, F., Yao, H., Li, H., & Tuan, R. S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.626708 · Cited by 31 · see citing works

Lineage-specific differences and regulatory networks governing human chondrocyte development

Richard, D. J., Pregizer, S. K., Venkatasubramanian, D., Raftery, R. M., Muthuirulan, P., Liu, Z., Capellini, T. D., & Craft, A. M. (2023) · eLife · doi:10.7554/elife.79925 · Cited by 25 · see citing works

Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease

Roberts, J. B., & Rice, S. J. (2024) · Current Rheumatology Reports · doi:10.1007/s11926-024-01142-z · Cited by 17 · see citing works

Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development

Darbellay, F., Ramisch, A., Lopez‐Delisle, L., Kosicki, M., Rauseo, A., Jouini, Z., Visel, A., & Andrey, G. (2024) · Nature Communications · doi:10.1038/s41467-024-49203-2 · Cited by 17 · see citing works

Inhibition of histone lysine demethylase 6A promotes chondrocytic activity and attenuates osteoarthritis development through repressing H3K27me3 enhancement of Wnt10a

Lian, W., Wu, R., Ko, J., Chen, Y., Wang, S.-Y., Jahr, H., & Wang, F. (2023) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2023.106394 · Cited by 14 · see citing works

Integrative approaches based on genomic techniques in the functional studies on enhancers

Wang, Q., Zhang, J., Liu, Z., Duan, Y., & Li, C. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad442 · Cited by 10 · see citing works

SERPINA3 is a marker of cartilage differentiation and is essential for the expression of extracellular matrix genes during early chondrogenesis

Barter, M. J., Turner, D. A., Rice, S. J., Hines, M., Lin, H., Falconer, A. M. D., McDonnell, E., Soul, J., Arques, M. D. C., Europe‐Finner, G. N., et al. (2024) · Matrix Biology · doi:10.1016/j.matbio.2024.07.004 · Cited by 8 · see citing works

Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints

Nowosad, K., Brouwer, R. W. W., Odrzywolski, A., Korporaal, A. L., Gielniewski, B., Wojtaś, B., van IJcken, W. F. J., Grosveld, F. G., Huylebroeck, D., & Tylżanowski, P. (2022) · Scientific Reports · doi:10.1038/s41598-022-16951-4 · Cited by 5 · see citing works

Genetic and functional analysis of ZMIZ1 in neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies (NEDDFSA): insights from muscle cells and signaling pathways

Li, S., Zhou, D., Han, Y., Feng, C., Lv, X., Fu, G., Wei, X., Wu, C., Yu, C., & Yang, Z. (2025) · Pediatric Research · doi:10.1038/s41390-025-04612-x · Cited by 3 · see citing works

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

Barter, M. J., Soul, J., Cheung, K., Falk, J., Putri, K., Farrier, A. J., Panagiotopoulos, A., Deehan, D. J., Reynard, L. N., & Young, D. A. (2026) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2025.12.015 · Cited by 3 · see citing works

SOX9 acts as a dynamic pioneer factor inducing stable changes in the chromatin landscape to reprogram endothelial cellsPreprint

Fuglerud, B. M., Drissler, S., Lotto, J., Stephan, T. L., Thakur, A., Cullum, R. L., & Hoodless, P. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.11.293993 · Cited by 2 · see citing works

The gene-regulatory evolution of the human skeleton

Yan, Y., Mishol, N., Lange, K., Zhang, Z., Bodek, G., Kigel, A., Priel, N., Egyes, N., Ronen, O., Nini, I., et al. (2026) · Nature · doi:10.1038/s41586-026-11053-x · Cited by 1 · see citing works

Étude du rôle des mécanismes épigénétiques dans la transition des cellules stromales mésenchymateuses en fibroblastes associés au cancer et dans l’acquisition de leurs propriétés pro-tumorales dans le lymphome folliculaire

Barbier, N. (2024) · theses.fr (ABES) · doi:10.70675/99c2b3c5z36bdz42fdz9878z99a368eb72e3

The biogenesis of extrachromosomal circular DNA is associated with enhancer-promoter dynamics and chromatin architecture

Gu, Y., Song, Y., Wang, S., Wang, Y., Zhao, Z., & Liu, J. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.152307

Chromatin remodeling and epigenetic regulation of mesenchymal stem/stromal cells in osteoarthritis

Wu, M., Sheng, C., Zhang, H., Chen, Y., Ma, T., Tong, Y., Xu, P., Tong, P., & Xia, H. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2026.1877252

Differentiating induced pluripotent stem cells into articular chondrocytes: advances, challenges, and future directions

Che, X., Jin, X., Lee, D.-K., Park, M. S., Kim, Y., Kim, H.-J., Kim, H.-J., & Choi, J. (2026) · Organoid · doi:10.51335/organoid.2026.6.e12

Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells

Herlofsen, S. R., Bryne, J. C., Høiby, T., Wang, L., Issner, R., Zhang, X., Coyne, M. J., Boyle, P., Gu, H., Meza‐Zepeda, L. A., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-105 · Cited by 79 · see citing works

Epigenetic regulation of chondrocyte differentiation

Thiesen, A. M. (2016) · DuEPublico (University of Duisburg-Essen)

Epigenetic Mechanisms Mediating Cell State Transitions in Chondrocytes

Wuelling, M., Neu, C., Thiesen, A. M., Kitanovski, S., Cao, Y., Lange, A., Westendorf, A. M., Hoffmann, D. E., & Vortkamp, A. (2020) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.4263 · Cited by 5 · see citing works

DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions

Barter, M. J., Bui, C., Cheung, K., Falk, J., Gómez, R., Skelton, A. J., Elliott, H. R., Reynard, L. N., & Young, D. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-58093-5 · Cited by 27 · see citing works

Histone methylation as a marker of chondrocyte phenotype

Wang, J., Kummer, S., Cosgrove, M. S., & Henderson, J. H. (2012) · IEEE Annual Northeast Bioengineering Conference (NEBEC) · doi:10.1109/nebc.2012.6207029 · Cited by 1 · see citing works