Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

Abstract

Alternative splicing is the main mechanism of increasing the proteome diversity coded by a limited number of genes. It is well established that different tissues or organs express different splicing variants. However, organs are composed of common major cell types, including fibroblasts, epithelial, and endothelial cells. By analyzing large-scale data sets generated by The ENCODE Project Consortium and after extensive RT-PCR validation, we demonstrate that each of the three major cell types expresses a specific splicing program independently of its organ origin. Furthermore, by analyzing splicing factor expression across samples, publicly available splicing factor binding site data sets (CLIP-seq), and exon array data sets after splicing factor depletion, we identified several splicing factors, including ESRP1 and 2, MBNL1, NOVA1, PTBP1, and RBFOX2, that contribute to establishing these cell type-specific splicing programs. All of the analyzed data sets are freely available in a user-friendly web interface named FasterDB, which describes all known splicing variants of human and mouse genes and their splicing patterns across several dozens of normal and cancer cells as well as across tissues. Information regarding splicing factors that potentially contribute to individual exon regulation is also provided via a dedicated CLIP-seq and exon array data visualization interface. To the best of our knowledge, FasterDB is the first database integrating such a variety of large-scale data sets to enable functional genomics analyses at exon-level resolution.[Supplemental material is available for this article.]Human genes are an assemblage of exons that can be differentially selected during splicing. Alternative splicing, which can produce splicing variants with different exonic content from a single gene, is the rule rather than an exception, as 95% of human genes generate several splicing variants (Kim et al. 2008;Hallegger et al. 2010;Kalsotra and Cooper 2011;Blencowe 2012;Kelemen et al. 2013). Alternative splicing relies on the combinatory action of splicing factors (e.g., SR and hnRNP proteins) that bind to exonic or intronic splicing regulatory sequences to either strengthen or inhibit splice site recognition by the splicing machinery, therefore enhancing or repressing the inclusion of alternative exons (Barash et al. 2010;Goren et al. 2010;Witten and Ule 2011). Similarly to how transcription factors control transcriptional programs by directing the expression of gene networks, splicing factors control splicing programs by regulating alternative splicing of co-regulated exons (Hartmann and Valcarcel 2009;Barash et al.

Identification of protein features encoded by alternative exons using Exon Ontology

“…1B; Mallinjoud et al 2014). In so doing, FasterDB genomic exons were associated with one or several EXONT terms and a web interface was developed in order to easily retrieve the EXONT terms associated with genomic exons (Fig.…”

“…For example, the selective expression of protein isoforms plays a major role in the biological functions of epithelial and mesenchymal cells, which are two major cell types found in many tissues (Bebee et al 2014;Mallinjoud et al 2014;Yang et al 2016b). Epithelial and mesenchymal cells ensure different physiological functions (epithelial cells are interconnected and nonmotile cells, while mesenchymal cells are isolated and motile cells), and the epithelial-to-mesenchymal transition has been shown to contribute to metastasis formation during tumor progression (Bebee et al 2014;Yang et al 2016b).…”

“…Epithelial and mesenchymal cells ensure different physiological functions (epithelial cells are interconnected and nonmotile cells, while mesenchymal cells are isolated and motile cells), and the epithelial-to-mesenchymal transition has been shown to contribute to metastasis formation during tumor progression (Bebee et al 2014;Yang et al 2016b). Several splicing factors, including ESRP1, ESRP2, RBM47, and RBFOX2, control the exon inclusion rate in an epithelial cell-or mesenchymal cell-specific manner, leading to the production of protein isoforms driving biological processes like cell polarity, adhesion, or motility (Venables et al 2013;Bebee et al 2014;Mallinjoud et al 2014;Vanharanta et al 2014;Yang et al 2016b).…”

A recently evolved class of alternative 3′-terminal exons involved in cell cycle regulation by topoisomerase inhibitors

“…Exon-array data were analysed with Expression Console (Affymetrix) to perform quality assessment and normalized using quintile normalization. Background correction and probe selection were performed as previously described, using exon annotation from the Faster DB database 22,60 (http://fasterdb.lyon.unicancer.fr/). Global gene regulation was calculated based on exonic probes from the whole gene.…”

Implications of NOVA1 suppression within the microenvironment of gastric cancer: association with immune cell dysregulation

“…A recent study revealed that NOVA1 is enriched in normal fibroblasts, suggesting involvement in the splicing programs of normal fibroblasts [10]. We previously noted that NOVA1 is expressed in only a small number of T cells within normal physiologic secondary lymphoid structures such as the palatine tonsils [11] .…”