Regulation of enhancers, co-expression domains and splicing efficiency by TGFß

Abstract

TGFβ cytokines have crucial roles in development, proliferation, tissue homeostasis, differentiation and immune regulation. Consequently, alterations in TGFβ signaling underlie numerous diseases, including cancer. TGFβ is one of the most potent inductors of epithelial to mesenchymal transition (EMT) in normal and oncogenic epithelial cells from different origins. EMT and its reversion (MET) are common processes during embryonic development and have attracted considerable interest due to the fact that they seem to be related to tumor cells dissemination and migration, generation of tumor circulating cells, cancer stem cells and metastasis formation. TGFβ causes a large reorganization of gene expression patterns and epigenetic information, that we are only starting to understand. In our group we are investigating how TGFβ causes these reorganization of gene expression patterns. We have cartographied the genomic transcriptional enhancers that are regulated by TGFβ in a breast epithelial cell line. In fact, TGFβ triggers a fast and widespread increase in chromatin accessibility in about 80% of enhancers, irrespective of whether they are activated, repressed or not regulated by TGFβ. We have also shown that most TGFβ-regulated genes are located around enhancers regulated in the same way, often creating domains of several co-regulated genes that we term TGFβ regulatory domains (TRD). We are currently investigating how the 3D organization of the genome connect the enhancers with the TRDs. We have also investigated whether regulation co-transcriptional splicing efficiency at the whole gene level is used to regulate gene expression by TGFβ. First we found that the existence of two well-differentiated strategies for co-transcriptional splicing efficiency, at the extremes of a gradient: short genes, that produces high levels of pre-mRNA display a relatively inefficient splicing while long genes with relatively low pre-mRNA levels present efficient splicing. Furthermore, we found that the TGFβ pathway regulates the general co-transcriptional splicing efficiency causing changes in mature mRNA levels. Taken together, our data indicate that co-transcriptional splicing efficiency is a gene-specific characteristic that can be regulated to control gene expression. Finally, other members of the group are looking for chromatin factors that control gene expression changes caused by TGFβ.