دورية أكاديمية
Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity.
| العنوان: | Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity. |
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| المؤلفون: | Cheung K; Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.; Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK., Barter MJ; Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK., Falk J; Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK., Proctor CJ; Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK., Reynard LN; Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK., Young DA; Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK. |
| المصدر: | FASEB journal : official publication of the Federation of American Societies for Experimental Biology [FASEB J] 2020 Apr; Vol. 34 (4), pp. 5317-5331. Date of Electronic Publication: 2020 Feb 14. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Federation of American Societies for Experimental Biology Country of Publication: United States NLM ID: 8804484 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1530-6860 (Electronic) Linking ISSN: 08926638 NLM ISO Abbreviation: FASEB J Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2020- : [Bethesda, Md.] : Hoboken, NJ : Federation of American Societies for Experimental Biology ; Wiley Original Publication: [Bethesda, Md.] : The Federation, [c1987- |
| مواضيع طبية MeSH: | Chondrogenesis* , Enhancer Elements, Genetic* , Epigenesis, Genetic*, Chondrocytes/*cytology , Chromatin/*genetics , Histones/*genetics , SOX9 Transcription Factor/*metabolism, Adult ; Cell Differentiation ; Cell Lineage ; Cells, Cultured ; Chondrocytes/metabolism ; Chromatin/metabolism ; Chromatin Immunoprecipitation Sequencing ; DNA Methylation ; Epigenomics ; Female ; Histones/metabolism ; Humans ; Promoter Regions, Genetic ; SOX9 Transcription Factor/genetics ; Young Adult |
| مستخلص: | Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) was used to assess a range of N-terminal posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP-seq and cis-regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis-related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de-methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell-types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell-types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross-talk between different epigenetic mechanisms during chondrocyte differentiation. (© 2020 The Authors. The FASEB Journal published by Wiley Periodicals, Inc. on behalf of Federation of American Societies for Experimental Biology.) |
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| معلومات مُعتمدة: | 18746 United Kingdom ARC_ Arthritis Research UK; 18746 United Kingdom VAC_ Versus Arthritis; United Kingdom DH_ Department of Health; 19424 United Kingdom VAC_ Versus Arthritis; MR/P020941/1 United Kingdom MRC_ Medical Research Council; 19424 United Kingdom ARC_ Arthritis Research UK; R476/0516 United Kingdom DMT_ The Dunhill Medical Trust |
| فهرسة مساهمة: | Keywords: cartilage; chondrocyte development; chromatin |
| المشرفين على المادة: | 0 (Chromatin) 0 (Histones) 0 (SOX9 Transcription Factor) 0 (SOX9 protein, human) |
| تواريخ الأحداث: | Date Created: 20200215 Date Completed: 20210119 Latest Revision: 20211006 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC7187454 |
| DOI: | 10.1096/fj.201902061RR |
| PMID: | 32058623 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1530-6860 |
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| DOI: | 10.1096/fj.201902061RR |