Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [ATAC-seq_2]

TGFß cytokines have crucial roles in development, proliferation, tissue homeostasis, differentiation, and immune regulation. Consequently, alterations in TGFß signaling underlie numerous diseases, including cancer. Moreover TGFß 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 TGFß, the chromatin dynamics during this process, or the SMAD (main effectors of TGFß pathway) partners in epithelial cells. To address these outstanding questions about the genomic regulation mediated by TGFß in epithelial cells we determine and characterize the enhancer atlas of the TGFß response in normal murine mammary gland (NMuMG) epithelial cells, a well-established model for TGFß-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 TGFß 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 TGFß treatment. We show that TGFß 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 TGFß-regulated enhancers revealed TGFß 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. Overall design: ATAC-seq analysis of NMuMG mouse glandular epithelial cells treated with TGFß1 at 10 minutes or 2 hours with vehicle as control (in starvation or complete medium conditions respectively) were generated by deep sequencing, in duplicates, using Illumina HiSeq2000.