Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.
1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5T 3H7, Canada.
Nature. 2014 Dec 11;516(7530):198-206. doi: 10.1038/nature14046.
Somatic cell reprogramming to a pluripotent state continues to challenge many of our assumptions about cellular specification, and despite major efforts, we lack a complete molecular characterization of the reprograming process. To address this gap in knowledge, we generated extensive transcriptomic, epigenomic and proteomic data sets describing the reprogramming routes leading from mouse embryonic fibroblasts to induced pluripotency. Through integrative analysis, we reveal that cells transition through distinct gene expression and epigenetic signatures and bifurcate towards reprogramming transgene-dependent and -independent stable pluripotent states. Early transcriptional events, driven by high levels of reprogramming transcription factor expression, are associated with widespread loss of histone H3 lysine 27 (H3K27me3) trimethylation, representing a general opening of the chromatin state. Maintenance of high transgene levels leads to re-acquisition of H3K27me3 and a stable pluripotent state that is alternative to the embryonic stem cell (ESC)-like fate. Lowering transgene levels at an intermediate phase, however, guides the process to the acquisition of ESC-like chromatin and DNA methylation signature. Our data provide a comprehensive molecular description of the reprogramming routes and is accessible through the Project Grandiose portal at http://www.stemformatics.org.
体细胞重编程为多能状态仍然挑战着我们对细胞特化的许多假设，尽管付出了巨大努力，我们仍然缺乏对重编程过程的完整分子特征描述。为了填补这一知识空白，我们生成了大量描述从小鼠胚胎成纤维细胞到诱导多能性的重编程途径的转录组、表观基因组和蛋白质组数据集。通过综合分析，我们揭示了细胞通过不同的基因表达和表观遗传特征转变，并向依赖和不依赖重编程转基因的稳定多能状态分叉。早期转录事件由高水平的重编程转录因子表达驱动，与广泛的组蛋白 H3 赖氨酸 27（H3K27me3）三甲基化丧失有关，代表了染色质状态的普遍开放。高转基因水平的维持导致 H3K27me3 的重新获得和稳定的多能状态，这是胚胎干细胞（ESC）样命运的替代。然而，在中间阶段降低转基因水平会指导该过程获得 ESC 样染色质和 DNA 甲基化特征。我们的数据提供了重编程途径的全面分子描述，并可通过 Project Grandiose 门户（http://www.stemformatics.org）访问。
