Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
Hepatology. 2019 Oct;70(4):1360-1376. doi: 10.1002/hep.30631. Epub 2019 May 15.
Cell-fate determination is influenced by interactions between master transcription factors (TFs) and cis-regulatory elements. Hepatocyte nuclear factor 4 alpha (HNF4A), a liver-enriched TF, acts as a master controller in specification of hepatic progenitor cells by regulating a network of TFs to control onset of hepatocyte cell fate. Using analysis of genome-wide histone modifications, DNA methylation, and hydroxymethylation in mouse hepatocytes, we show that HNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially acetylation of lysine 27 of histone 3 (H3K27ac) and 5-hydroxymethylcytosine (5hmC). In mice lacking HNF4A protein in hepatocytes, we observed a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A. Mechanistically, HNF4A-associated hydroxymethylation (5hmC) requires its interaction with ten-eleven translocation methylcytosine dioxygenase 3 (TET3), a protein responsible for oxidation from 5mC to 5hmC. Furthermore, HNF4A regulates TET3 expression in liver by directly binding to an enhancer region. Conclusion: In conclusion, we identified that HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes.
细胞命运的决定受到主转录因子（TFs）与顺式调控元件之间相互作用的影响。肝核因子 4 阿尔法（HNF4A）是一种富含肝脏的 TF，通过调节 TF 网络来控制肝祖细胞的起始命运，充当肝脏祖细胞特化的主控控制器。通过对小鼠肝细胞全基因组组蛋白修饰、DNA 甲基化和羟甲基化的分析，我们表明 HNF4A 占据了肝细胞中的活性增强子，并且对于活性组蛋白和 DNA 特征（特别是组蛋白 3 赖氨酸 27 的乙酰化（H3K27ac）和 5-羟甲基胞嘧啶（5hmC））是必需的。在缺乏肝细胞中 HNF4A 蛋白的小鼠中，我们观察到 HNF4A 结合区域的 H3K27ac 和羟甲基化水平均降低。从机制上讲，HNF4A 相关的羟甲基化（5hmC）需要其与十号染色体缺失蛋白 3（TET3）相互作用，TET3 是一种负责将 5mC 氧化为 5hmC 的蛋白。此外，HNF4A 通过直接结合增强子区域来调节肝脏中 TET3 的表达。结论：总之，我们确定 HNF4A 是肝细胞中增强子上活跃的表观遗传状态所必需的，这种状态可扩增基因的转录。
