Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [ChIP-seq]

TGFβ cytokines have crucial roles in development, proliferation, tissue homeostasis, differentiation, and immune regulation. Consequently, alterations in TGFβ signaling underlie numerous diseases, including cancer. Moreover TGFβ is one of the most potent inductors of EMT (epithelial to mesenchymal transition) in normal and oncogenic epithelial cells from different origins. During EMT, cells undergo an extensive reorganization of cell adhesion complexes, cytoskeletal architecture, and extracellular matrix interactions and acquire increased motility and invasion properties. However, little is known about the genomic repertoire of enhancers activated by TGFβ, the chromatin dynamics during this process, or the SMAD (main effectors of TGFβ pathway) partners in epithelial cells. To address these outstanding questions about the genomic regulation mediated by TGFβ in epithelial cells we determine and characterize the enhancer atlas of the TGFβ response in normal murine mammary gland (NMuMG) epithelial cells, a well-established model for TGFβ-dependent EMT. To achieve this we performed ATAC-seq, ChIP-seq against typical histone modifications for enhancers and promoters (H3K27ac, H3K4me1 and H3K4me3) and ChromRNA-seq (to identify enhancer RNAs) analyses at two different time points after TGFβ treatment (2h and 12h) to study the enhancers dynamics during this process. We also performed a transcriptomic analyses (RNA-seq) at same time points to correlate genomic regulation to transcriptional changes upon TGFβ treatment. We show that TGFβ promotes a fast and widespread increase of chromatin accessibility in most enhancers of the cell line, irrespectively of whether the enhancer will become activated or repressed. We also observed that activated enhancers are strongly enriched for SMAD2/3/4 and AP-1 footprints. In contrast, decommissioned enhancers present footprints for TEAD, HNF1A, or HNF1B TF (and not for SMAD2/3/4). Strikingly, analyses of the regulated genes around TGFβ-regulated enhancers revealed TGFβ regulatory domains that can encompass several genes and that are constrained by 3D chromatin conformation. In these domains enhancer targeting is more promiscuous than previously anticipated. Binding profiles of H3K27ac, H3K4me1 and H3K4me3 from NMuMG mouse glandular epithelial cells treated with TGFβ1 at 2h and 12h or with vehicle as control were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.