Analysis of epigenetic features of mouse Meckel’s cartilage by integrating multi-omics data

doi:10.19439/j.sjos.2026.02.001

Abstract

Abstract: PURPOSE: To characterize the epigenetic features of mouse Meckel's cartilage and potential gene expression regulation mechanisms based on multi-omics data. METHODS: E14.5 Meckel's cartilage and forelimb cartilage multi-omics data in our group were incorporated, and published datasets of a wide range of mouse chondrocytes from the GEO database were also downloaded. Bioinformatics methods were used to compare chromatin accessibility, histone acetylation modifications, as well as three-dimensional genomic structural differences between different chondrocyte samples. Results: ATAC-seq analysis results showed that E14.5 Meckel's cartilage exhibited a more similar chromatin accessibility pattern to epiphyseal cartilage. CUT&Tag analysis results showed that H3K27ac modification level of 11 899 peaks differed significantly between Meckel's cartilage and forelimb cartilage, and acetylation modifications in 8 572 peaks were upregulated in Merkel's cartilage. Motif analysis results showed that the up-regulated H3K27ac peaks in Meckel's cartilage were enriched with Fos, Atf3, and AP-1 binding sites. Integration analysis of CUT&Tag and Hi-C results indicated the presence of chromatin loop-mediated promoter-super-enhancer interactions at the loci of Runx2 and Six2. CONCLUSIONS: E14.5 Meckel's cartilage mainly exhibits chromatin accessibility characteristics of proliferative chondrocytes. Transcription factors such as Fos, and Six2 may play an important role in the transcriptional regulation of Meckel's cartilage development during the proliferative stage. Changes in chromatin epigenetic modifications associated with hypertrophy of Meckel's cartilage may appear gradually during the later stage of Merkel's cartilage development.

Key words: Meckel's cartilage, Epigenetics, 3D-Genomics, mandibular development, Craniomaxillofacial surgery

CLC Number:

R782.6

Pan Zhiyuan, Wang Hongwei, Cheng Li, Lin Guofen, Dai Jiewen. Analysis of epigenetic features of mouse Meckel’s cartilage by integrating multi-omics data[J]. Shanghai Journal of Stomatology, 2026, 35(2): 113-120.

References

[1] Svandova E, Anthwal N, Tucker AS, et al.Diverse fate of an enigmatic structure: 200 years of Meckel's cartilage[J]. Front Cell Dev Biol, 2020, 8: 821.
[2] Fernández-Rubio EM, Radlanski RJ.Development of the primary and secondary jaw joints in the mouse[J]. Ann Anat, 2023, 249: 152085.
[3] Fernández-Rubio EM, Radlanski RJ.Development of the human primary and secondary jaw joints[J]. Ann Anat, 2024, 251: 152169.
[4] Sakakura Y, Hosokawa Y, Tsuruga E, et al.In situ localization of gelatinolytic activity during development and resorption of Meckel's cartilage in mice[J]. Eur J Oral Sci, 2007, 115(3): 212-223.
[5] Yang RT, Zhang C, Liu Y, et al.Autophagy prior to chondrocyte cell death during the degeneration of Meckel's cartilage[J]. Anat Rec (Hoboken), 2012, 295(5): 734-741.
[6] Anthwal N, Urban DJ, Luo ZX, et al.Meckel's cartilage breakdown offers clues to mammalian middle ear evolution[J]. Nat Ecol Evol, 2017, 1(4): 93.
[7] Mao F, Zhang C, Ren J, et al.Fossils document evolutionary changes of jaw joint to mammalian middle ear[J]. Nature, 2024, 628(8008): 576-581.
[8] Melnick M, Witcher D, Bringas P Jr, et al.Meckel's cartilage differentiation is dependent on hedgehog signaling[J]. Cells Tissues Organs, 2005, 179(4): 146-157.
[9] Pitirri MK, Durham EL, Romano NA, et al.Meckel's cartilage in mandibular development and dysmorphogenesis[J]. Front Genet, 2022, 13: 871927.
[10] Minoux M, Holwerda S, Vitobello A, et al. Gene bivalency at Polycomb domains regulates cranial neural crest positional identity[J]. Science, 2017, 355(6332): eaal2913.
[11] He P, Williams BA, Trout D, et al.The changing mouse embryo transcriptome at whole tissue and single-cell resolution[J]. Nature, 2020, 583(7818): 760-767.
[12] Richard D, Liu Z, Cao J, et al. Evolutionary selection and constraint on human knee chondrocyte regulation impacts osteoarthritis risk[J]. Cell, 2020, 181(2): 362-381.e28.
[13] Chen Y, Yu Y, Wen Y, et al.A high-resolution route map reveals distinct stages of chondrocyte dedifferentiation for cartilage regeneration[J]. Bone Res, 2022, 10(1): 38-54.
[14] Chen Q, Dai J, Bian Q. Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects[J]. Sci Adv, 2022, 8(47): eabo3648.
[15] Grandi FC, Modi H, Kampman L, et al.Chromatin accessibility profiling by ATAC-seq[J]. Nat Protoc, 2022, 17(6): 1518-1552.
[16] Cheng S, Miao B, Li T, et al. Review and evaluate the bioinformatics analysis strategies of ATAC-seq and CUT&Tag data[J]. Genomics Proteomics Bioinformatics, 2024, 22(3): qzae054.
[17] Li F, Tian J, Zhang L, et al.A multi-omics approach to reveal critical mechanisms of activator protein 1 (AP-1)[J]. Biomed Pharmacother, 2024, 178: 117225.
[18] Kravchuk EV, Ashniev GA, Gladkova MG, et al.Experimental validation and prediction of super-enhancers: advances and challenges[J]. Cells, 2023, 12(8): 1191.
[19] Yang JH, Hansen AS.Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation[J]. Nat Rev Mol Cell Biol, 2024, 25(7): 574-591.
[20] Zhu J, Luo Q, Cao T, et al. Injectable cartilage microtissues based on 3D culture using porous gelatin microcarriers for cartilage defect treatment[J]. Regen Biomater, 2024, 11: rbae064.
[21] Alizadeh Sardroud H, Rosa GDS, Dust W, et al.Comparison study on hyaline cartilage versus fibrocartilage formation in a pig model by using 3D-bioprinted hydrogel and hybrid constructs[J]. Biofabrication, 2024, 17(1): 015014.
[22] Kitami M, Kaku M, Thant L, et al.A loss of primary cilia by a reduction in mTOR signaling correlates with age-related deteriorations in condylar cartilage[J]. Geroscience, 2024, 46(6): 5995-6007.
[23] Ukita M, Matsushita K, Tamura M, et al.Histone H3K9 methylation is involved in temporomandibular joint osteoarthritis[J]. Int J Mol Med, 2020, 45(2): 607-614.
[24] Yao Y, Wang Y.ATDC5: an excellent in vitro model cell line for skeletal development[J]. J Cell Biochem, 2013, 114(6): 1223-1229.
[25] Wilhelm D, Kempf H, Bianchi A, et al.ATDC5 cells as a model of cartilage extracellular matrix neosynthesis, maturation and assembly[J]. J Proteomics, 2020, 219: 103718.
[26] Paesa M, Ancín-Azpilicueta C, Velderrain-Rodríguez G, et al.Anti-Inflammatory and chondroprotective effects induced by phenolic compounds from onion waste extracts in ATDC-5 chondrogenic cell line[J]. Antioxidants (Basel), 2022, 11(12): 2381.
[27] Caron MMJ, Eveque M, Cillero-Pastor B, et al.Sox9 determines translational capacity during early chondrogenic differentiation of ATDC5 cells by regulating expression of ribosome biogenesis factors and ribosomal proteins[J]. Front Cell Dev Biol, 2021, 9: 686096.
[28] Steinbusch MMF, van den Akker GGH, Cremers A, et al. Adaptation of the protein translational apparatus during ATDC5 chondrogenic differentiation[J]. Noncoding RNA Res, 2022, 7(2): 55-65.
[29] Metz R, Bannister AJ, Sutherland JA, et al.c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein[J]. Mol Cell Biol, 1994, 14(9): 6021-6029.
[30] Kurlishchuk Y, Cindric Vranesic A, Jessen M, et al.A non-canonical repressor function of JUN restrains YAP activity and liver cancer growth[J]. EMBO J, 2024, 43(20): 4578-4603.
[31] Iitsuka N, Hie M, Tsukamoto I.Zinc supplementation inhibits the increase in osteoclastogenesis and decrease in osteoblastogenesis in streptozotocin-induced diabetic rats[J]. Eur J Pharmacol, 2013, 714(1-3): 41-47.
[32] Wu Z, Nicoll M, Ingham RJ.AP-1 family transcription factors: a diverse family of proteins that regulate varied cellular activities in classical hodgkin lymphoma and ALK+ ALCL[J]. Exp Hematol Oncol, 2021, 10(1): 4-16.
[33] Sladitschek HL, Neveu PA.A gene regulatory network controls the balance between mesendoderm and ectoderm at pluripotency exit[J]. Mol Syst Biol, 2019, 15(12): e9043.
[34] Feldker N, Ferrazzi F, Schuhwerk H, et al.Genome-wide cooperation of EMT transcription factor ZEB1 with YAP and AP-1 in breast cancer[J]. EMBO J, 2020, 39(17): e103209.
[35] Wang J, Young IG.Eosinophilic inflammation: mechanisms regulating IL-5 transcription in human T lymphocytes[J]. Allergy, 2007, 62(10): 1131-1138.
[36] Yu G, Wang LG, He QY.ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization[J]. Bioinformatics, 2015, 31(14): 2382-2383.
[37] Xie L, Wu S, He R, et al.Identification of epigenetic dysregulation gene markers and immune landscape in kidney renal clear cell carcinoma by comprehensive genomic analysis[J]. Front Immunol, 2022, 13: 901662.