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Mechanisms of species and cell-type specific splicing regulation

In addition to functional studies, we are investigating mechanisms that lead to distinct splicing patterns in different cell types, as a function of external stimuli or in a species-specific manner. Using minigene analyses and RNA-protein interaction methods such as X-link, pull-down and CLIP, we are aiming to characterize the cis- and trans-acting elements as well as signaling cascades that mediate splicing regulation of functionally important target genes. To be able to identify trans-regulatory proteins for a particular splicing event without analyzing cis-acting elements beforehand, we have established a targeted siRNA screen in mouse and human cells. We have acquired siRNA libraries that target around 200 (human) or 100 (mouse) splicing regulatory proteins and have successfully used these libraries in different cellular backgrounds to identify trans-acting factors that control alternative splicing of exons we and other groups are interested in (e.g. Meiniger et al., 2016, Nat Comm; Schultz et al., 2016, MCB).
 

Identification of Celf2 as a trans-acting factor that controls Traf3 alternative splicing upon T cell activation using an siRNA screen (Schultz et al., 2016, MCB).
 

As several of our target exons appear to be regulated in a species-specific manner, we have started to analyze alternative splicing patterns of orthologous exons in different species more systematically. For some targets we use minigene assays to investigate how species-specific splicing patterns are established. These analyses form the basis to investigate the functionality of species-specific alternative splicing and a potential role in defining species-specific traits.