Genome-wide identification of alternative splicing events that regulate protein transport across the secretory pathway

Abstract

Alternative splicing (AS) strongly increases proteome diversity and functionality in eukaryotic cells. Protein secretion is a tightly-controlled process, especially in a tissue-specific and differentiation-dependent manner. While previous work has focussed on transcriptional and posttranslational regulatory mechanisms, the impact of AS on the secretory pathway remains largely unexplored. Here we integrate a published screen for modulators of protein transport and RNA-Seq analyses to identify over 200 AS events as secretion regulators. We confirm that splicing events along all stages of the secretory pathway regulate the efficiency of protein transport using Morpholinos and CRISPR/Cas9. We furthermore show that these events are highly tissue-specific and adapt the secretory pathway during T-cell activation and adipocyte differentiation. Our data substantially advance the understanding of AS functionality, add a new regulatory layer to a fundamental cell biological process and provide a resource of alternative isoforms that control the secretory pathway.

In silico analysis of alternative splicing events implicated in intracellular trafficking during B-lymphocyte differentiation

“…These analyses together indicate that alternative splicing controls diverse trafficking pathways during B cell activation and differentiation. Furthermore, the adaptation of intracellular trafficking in B cell subsets is different from the situation observed during T cell activation, which largely relies on alternative splicing to control their secretory capacity (34,35). In addition, AS events that change in COPII genes during T-Lymphocyte activation and B-Lymphocyte differentiation are mostly different, pointing to largely different strategies to adapt the secretory machinery to changing conditions.…”

“…To better understand the mechanism that allows PCs to regulate their secretory machinery, we compared the expression level changes of COPII components in PCs and during the activation of CD4+ T cells (Figure 2G) (34). Interestingly, the expression of COPII components during T cell activation stays rather constant, whereas PCs show a substantial upregulation of almost all COPII components when compared to non-antibodysecreting prePB.…”

“…Interestingly, the expression of COPII components during T cell activation stays rather constant, whereas PCs show a substantial upregulation of almost all COPII components when compared to non-antibodysecreting prePB. These data suggest that B cells use changes in gene expression to adjust their secretory machinery during activation and differentiation, whereas T cells rely mostly on alternative splicing of key regulators (34,35). This may also indicate that B cells require stronger adjustments to their secretory system than T cells, which would make B cell differentiation a very interesting model system to study the adaptation of the secretory pathway in the future.…”