Sammons Morgan A, Zhu Jiajun, Drake Adam M, Berger Shelley L
Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res. 2015 Feb;25(2):179-88. doi: 10.1101/gr.181883.114. Epub 2014 Nov 12.
Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide data sets, we examined the relationship between TP53 binding and the dynamics of the local chromatin environment. Our analysis revealed three distinct categories of TP53 binding events that differ based on the dynamics of the local chromatin environment. The first class of TP53 binding events occurs near transcriptional start sites (TSS) and is defined by previously characterized promoter-associated chromatin modifications. The second class comprises a large cohort of preestablished, promoter-distal enhancer elements that demonstrates dynamic histone acetylation and transcription upon TP53 binding. The third class of TP53 binding sites is devoid of classic chromatin modifications and, remarkably, fall within regions of inaccessible chromatin, suggesting that TP53 has intrinsic pioneer factor activity and binds within structurally inaccessible regions of chromatin. Intriguingly, these inaccessible TP53 binding sites feature several enhancer-like properties in cell types within the epithelial lineage, indicating that TP53 binding events include a group of "proto-enhancers" that become active enhancers given the appropriate cellular context. These data indicate that TP53, along with TP63, may act as pioneer factors to specify epithelial enhancers. Further, these findings suggest that rather than following a global cell-type invariant stress response program, TP53 may tune its response based on the lineage-specific epigenomic landscape.
尽管有压倒性的证据表明TP53的转录激活对其肿瘤抑制活性至关重要,但TP53在染色质背景下与基因组结合以激活转录的机制仍未得到充分理解。我们使用了一系列新的和现有的全基因组数据集,研究了TP53结合与局部染色质环境动态之间的关系。我们的分析揭示了三类不同的TP53结合事件,它们根据局部染色质环境的动态而有所不同。第一类TP53结合事件发生在转录起始位点(TSS)附近,并由先前表征的启动子相关染色质修饰所定义。第二类包括大量预先存在的、启动子远端增强子元件,这些元件在TP53结合后表现出动态组蛋白乙酰化和转录。第三类TP53结合位点缺乏经典的染色质修饰,并且显著地落在难以接近的染色质区域内,这表明TP53具有内在的先锋因子活性,并结合在染色质的结构上难以接近的区域内。有趣的是,这些难以接近的TP53结合位点在上皮谱系的细胞类型中具有几种类似增强子的特性,这表明TP53结合事件包括一组“原增强子”,在适当的细胞背景下会成为活性增强子。这些数据表明,TP53与TP63一起可能作为先锋因子来指定上皮增强子。此外,这些发现表明,TP53可能不是遵循全球细胞类型不变的应激反应程序,而是根据谱系特异性表观基因组景观来调整其反应。