Alternative splicing (AS) programs are primarily controlled by regulatory RNA-binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.
Keywords: RNA binding protein; alternative splicing; chromosomes; gene expression; rat; smooth muscle; super-enhancer.
All the cells in our body contain the same genetic information, but they only switch on the genes that they need to fulfill their specific role in the organism. Genetic sequences known as enhancers can turn on the genes that are required by a particular cell to perform its tasks. Once a gene is activated, its sequence is faithfully copied into a molecule of RNA which contains segments that code for a protein. A molecular machine then processes the RNA molecule and splices together the coding segments. RNA binding proteins can also regulate this mechanism, and help to splice the coding sections in different ways depending on the type of cell. The process, known as alternative RNA splicing, therefore creates different RNA templates from the same gene. This gives rise to related but different proteins, each suited to the needs of the particular cell in which they are made. However, in some cell types, exactly how this happens has not yet been well documented. For example, in cells that line blood vessels – known as vascular smooth muscle cells – the RNA binding proteins that drive alternative splicing have not been identified. To find these proteins, Nakagaki-Silva et al. used catalogs of DNA regions called super-enhancers as clues. These sequences strongly activate certain genes in a tissue-specific manner, effectively acting as labels for genes important for a given cell type. In vascular smooth muscle cells, if a super-enhancer switches on a gene that codes for a RNA-binding protein, this protein is probably crucial for the cell to work properly. The approach highlighted a protein called RBPMS, and showed that it controlled alternative RNA splicing of many genes important in smooth muscle cells. This may suggest that when RBPMS regulation is disrupted, certain diseases of the heart and blood vessels could emerge. Finally, the results by Nakagaki-Silva et al. demonstrate that super-enhancers can signpost genes important in regulating splicing or other key processes in particular cell types.
© 2019, Nakagaki-Silva et al.