Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany.
Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany.
J Bone Miner Res. 2021 May;36(5):968-985. doi: 10.1002/jbmr.4263. Epub 2021 Mar 2.
Epigenetic modifications play critical roles in regulating cell lineage differentiation, but the epigenetic mechanisms guiding specific differentiation steps within a cell lineage have rarely been investigated. To decipher such mechanisms, we used the defined transition from proliferating (PC) into hypertrophic chondrocytes (HC) during endochondral ossification as a model. We established a map of activating and repressive histone modifications for each cell type. ChromHMM state transition analysis and Pareto-based integration of differential levels of mRNA and epigenetic marks revealed that differentiation-associated gene repression is initiated by the addition of H3K27me3 to promoters still carrying substantial levels of activating marks. Moreover, the integrative analysis identified genes specifically expressed in cells undergoing the transition into hypertrophy. Investigation of enhancer profiles detected surprising differences in enhancer number, location, and transcription factor binding sites between the two closely related cell types. Furthermore, cell type-specific upregulation of gene expression was associated with increased numbers of H3K27ac peaks. Pathway analysis identified PC-specific enhancers associated with chondrogenic genes, whereas HC-specific enhancers mainly control metabolic pathways linking epigenetic signature to biological functions. Since HC-specific enhancers show a higher conservation in postnatal tissues, the switch to metabolic pathways seems to be a hallmark of differentiated tissues. Surprisingly, the analysis of H3K27ac levels at super-enhancers revealed a rapid adaption of H3K27ac occupancy to changes in gene expression, supporting the importance of enhancer modulation for acute alterations in gene expression. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
表观遗传修饰在调节细胞谱系分化中起着关键作用，但指导细胞谱系内特定分化步骤的表观遗传机制很少被研究。为了解析这些机制，我们以软骨内骨化过程中增殖（PC）细胞向肥大（HC）细胞的特化作为模型。我们为每种细胞类型绘制了激活和抑制组蛋白修饰图谱。ChromHMM 状态转换分析和基于 Pareto 的差异水平 mRNA 和表观遗传标记的整合表明，分化相关基因的抑制是通过在仍保留大量激活标记的启动子上添加 H3K27me3 来启动的。此外，综合分析确定了在向肥大过渡过程中特异性表达的基因。增强子图谱的研究检测到两种密切相关的细胞类型之间在增强子数量、位置和转录因子结合位点上存在惊人的差异。此外，细胞类型特异性基因表达的上调与 H3K27ac 峰数量的增加有关。通路分析确定了与软骨基因相关的 PC 特异性增强子，而 HC 特异性增强子主要控制将表观遗传特征与生物学功能联系起来的代谢途径。由于 HC 特异性增强子在出生后组织中具有更高的保守性，因此向代谢途径的转变似乎是分化组织的标志。令人惊讶的是，超级增强子上 H3K27ac 水平的分析表明，H3K27ac 占据对基因表达变化的快速适应，支持增强子调节对于基因表达的急性改变的重要性。
