Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations. Here, we apply biological, biochemical, and network biology methods to validate GEMM-derived cell models using inducible KrasG12D expression. We describe the time-dependent, chromatin remodeling program that impacts function during early oncogenic signaling. We find that the KrasG12D-induced transcriptional response is dominated by downregulated expression concordant with layers of epigenetic events. More open chromatin characterizes the ATAC-seq profile associated with a smaller group of upregulated genes and epigenetic marks. RRBS demonstrates that promoter hypermethylation does not account for the silencing of the extensive gene promoter network. Moreover, ChIP-Seq reveals that heterochromatin reorganization plays little role in this early transcriptional program. Notably, both gene activation and silencing primarily depend on the marking of genes with a combination of H3K27ac, H3K4me3, and H3K36me3. Indeed, integrated modeling of all these datasets shows that KrasG12D regulates its transcriptional program primarily through unique super-enhancers and enhancers, and marking specific gene promoters and bodies. We also report chromatin remodeling across genomic areas that, although not contributing directly to cis-gene transcription, are likely important for KrasG12D functions. In summary, we report a comprehensive, time-dependent, and coordinated early epigenomic program for KrasG12D in pancreatic cells, which is mechanistically relevant to understanding chromatin remodeling events underlying transcriptional outcomes needed for the function of this oncogene.

中文翻译：

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KrasG12D 诱导染色质区域的变化，对胰腺细胞的早期核重编程产生不同的影响

胰腺导管腺癌的发生最常由 Kras 突变引起。在这里，我们应用生物、生化和网络生物学方法来验证使用诱导型 KrasG12D 表达的 GEMM 衍生细胞模型。我们描述了在早期致癌信号传导过程中影响功能的时间依赖性染色质重塑程序。我们发现 KrasG12D 诱导的转录反应主要是与表观遗传事件层一致的表达下调。更开放的染色质表征了与一小群上调基因和表观遗传标记相关的 ATAC-seq 图谱。RRBS 证明启动子高甲基化并不能解释广泛的基因启动子网络的沉默。此外，ChIP-Seq 揭示异染色质重组在这一早期转录程序中发挥的作用很小。值得注意的是，基因激活和沉默主要取决于 H3K27ac、H3K4me3 和 H3K36me3 组合的基因标记。事实上，所有这些数据集的综合建模表明，KrasG12D 主要通过独特的超级增强子和增强子以及标记特定的基因启动子和基因体来调节其转录程序。我们还报告了跨基因组区域的染色质重塑，虽然不直接促进顺式基因转录，但可能对 KrasG12D 功能很重要。总之，我们报告了胰腺细胞中 KrasG12D 的全面、时间依赖性和协调的早期表观基因组程序，该程序在机制上与理解该癌基因功能所需的转录结果背后的染色质重塑事件相关。