The myoblast methylome: multiple types of associations with chromatin and transcription

Epigenetic changes are implicated in development, repair, and physiology of postnatal skeletal muscle (SkM). We generated methylomes for human myoblasts (SkM progenitor cells) and determined myoblast differentially methylated regions (DMRs) for comparison to the epigenomics and transcriptomics of diverse cell types. Analyses were from global genomic and single-gene perspectives and included reporter gene assays. One atypical finding was the association of promoter-adjacent hypermethylation in myoblasts with transcription turn-on, but at downmodulated levels, for certain genes (e.g., SIM2 and TWIST1). In contrast, brain-specific OLIG2 was in repressed chromatin and silent in most cell types but linked to hypermethylated DMRs specifically in myoblasts. The OLIG2-linked DMRs might be needed because of the overlapping or nearby binding of myogenic differentiation protein 1 (MYOD). We found genome-wide overlap of DMRs with MYOD or CCCTC-binding factor (CTCF) binding sites in myoblasts that is consistent with the importance of MYOD, as well as CTCF, in organizing myoblast transcription-enhancing chromatin interactions. We also observed some gene upregulation correlated with a special association of regional DNA hypomethylation with H3K36me3, H3K27ac, and H3K4me1 enrichment. Our study highlights unusual relationships between epigenetics and gene expression that illustrate the interplay between DNA methylation and chromatin epigenetics in the regulation of transcription.表观遗传变化（Epigenetic changes）与出生后骨骼肌（postnatal skeletal muscle, SkM）的发育、修复及生理功能紧密相关。本研究针对人类成肌细胞（human myoblasts，即SkM祖细胞）构建了全基因组甲基化组，并鉴定了成肌细胞的差异甲基化区域（differentially methylated regions, DMRs），用于与多种细胞类型的表观基因组学（epigenomics）和转录组学（transcriptomics）数据开展对比分析。分析从全基因组与单基因两个维度展开，同时纳入了报告基因实验（reporter gene assays）。一项非典型发现为：部分基因（如SIM2与TWIST1）的成肌细胞启动子邻近区域高甲基化，与转录激活相关，但该激活处于下调水平。与之相反，脑特异性OLIG2在多数细胞类型中处于抑制性染色质（repressed chromatin）状态且呈沉默表达，却仅在成肌细胞中与高甲基化DMRs相关联。鉴于肌分化蛋白1（myogenic differentiation protein 1, MYOD）在OLIG2区域存在重叠或邻近结合，OLIG2关联的DMRs或为必需。本研究发现，成肌细胞中DMRs与MYOD或CCCTC结合因子（CCCTC-binding factor, CTCF）的结合位点在全基因组范围内存在重叠，这与MYOD及CTCF在调控成肌细胞转录增强型染色质相互作用中的重要作用相符。我们还观察到，部分基因的上调与区域DNA低甲基化及H3K36me3、H3K27ac、H3K4me1组蛋白修饰富集的特殊关联相关。本研究揭示了表观遗传与基因表达间的非典型关联，阐明了DNA甲基化与染色质表观遗传在转录调控中的相互作用机制。