Julian L M, Liu Y, Pakenham C A, Dugal-Tessier D, Ruzhynsky V, Bae S, Tsai S-Y, Leone G, Slack R S, Blais A
Neuroscience program, Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
Department of Biochemsitry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
Cell Death Differ. 2016 Apr;23(4):565-75. doi: 10.1038/cdd.2015.36. Epub 2015 Apr 24.
Cell cycle proteins are important regulators of diverse cell fate decisions, and in this capacity have pivotal roles in neurogenesis and brain development. The mechanisms by which cell cycle regulation is integrated with cell fate control in the brain and other tissues are poorly understood, and an outstanding question is whether the cell cycle machinery regulates fate decisions directly or instead as a secondary consequence of proliferative control. Identification of the genes targeted by E2 promoter binding factor (E2f) transcription factors, effectors of the pRb/E2f cell cycle pathway, will provide essential insights into these mechanisms. We identified the promoter regions bound by three neurogenic E2f factors in neural precursor cells in a genome-wide manner. Through bioinformatic analyses and integration of published genomic data sets we uncovered hundreds of transcriptionally active E2f-bound promoters corresponding to genes that control cell fate processes, including key transcriptional regulators and members of the Notch, fibroblast growth factor, Wnt and Tgf-β signaling pathways. We also demonstrate a striking enrichment of the CCCTC binding factor transcription factor (Ctcf) at E2f3-bound nervous system-related genes, suggesting a potential regulatory co-factor for E2f3 in controlling differentiation. Finally, we provide the first demonstration of extensive tissue specificity among E2f target genes in mammalian cells, whereby E2f3 promoter binding is well conserved between neural and muscle precursors at genes associated with cell cycle processes, but is tissue-specific at differentiation-associated genes. Our findings implicate the cell cycle pathway as a widespread regulator of cell fate genes, and suggest that E2f3 proteins control cell type-specific differentiation programs by regulating unique sets of target genes. This work significantly enhances our understanding of how the cell cycle machinery impacts cell fate and differentiation, and will importantly drive further discovery regarding the mechanisms of cell fate control and transcriptional regulation in the brain, as well as in other tissues.
细胞周期蛋白是多种细胞命运决定的重要调节因子，在此过程中对神经发生和大脑发育起着关键作用。目前，人们对大脑和其他组织中细胞周期调控与细胞命运控制整合的机制了解甚少，一个悬而未决的问题是细胞周期机制是直接调节命运决定，还是作为增殖控制的次要结果。鉴定E2启动子结合因子（E2f）转录因子（pRb/E2f细胞周期途径的效应器）的靶基因，将为这些机制提供重要见解。我们在全基因组范围内鉴定了神经前体细胞中三种神经源性E2f因子结合的启动子区域。通过生物信息学分析和整合已发表的基因组数据集，我们发现了数百个转录活性的E2f结合启动子，这些启动子对应于控制细胞命运过程的基因，包括关键转录调节因子以及Notch、成纤维细胞生长因子、Wnt和Tgf-β信号通路的成员。我们还证明了CCCTC结合因子转录因子（Ctcf）在E2f3结合的神经系统相关基因中显著富集，这表明Ctcf可能是E2f3控制分化的潜在调节辅助因子。最后，我们首次证明了哺乳动物细胞中E2f靶基因之间存在广泛的组织特异性，即E2f3启动子结合在与细胞周期过程相关的基因的神经和肌肉前体细胞之间保守性良好，但在与分化相关的基因中具有组织特异性。我们的研究结果表明细胞周期途径是细胞命运基因的广泛调节因子，并表明E2f3蛋白通过调节独特的靶基因集来控制细胞类型特异性分化程序。这项工作显著增强了我们对细胞周期机制如何影响细胞命运和分化的理解，并将重要地推动关于大脑以及其他组织中细胞命运控制和转录调节机制的进一步发现。
