Kras(G12D) induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells

BACKGROUND: Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations. RESULTS: Here, we apply biological, biochemical, and network biology methods to validate GEMM-derived cell models using inducible Kras(G12D) expression. We describe the time-dependent, chromatin remodeling program that impacts function during early oncogenic signaling. We find that the Kras(G12D)-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 Kras(G12D) 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 Kras(G12D) functions. CONCLUSIONS: In summary, we report a comprehensive, time-dependent, and coordinated early epigenomic program for Kras(G12D) in pancreatic cells, which is mechanistically relevant to understanding chromatin remodeling events underlying transcriptional outcomes needed for the function of this oncogene. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02498-6.