Function of SF1 protein variants in early spliceosome recruitment and splicing

• Applicant: Dr. Irene Beusch
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 571960582

Splicing is essential for eukaryotic gene expression. In humans it presents a unique challenge: exons must be identified within transcripts comprised of ~85% intronic sequences. It is even further complicated by alternative splicing. Therefore, where to splice presents not only a challenge, but also a significant opportunity for the cell to regulate gene expression. Splicing begins with the recognition of the splicing signals and de novo assembly of the splicing machinery, the spliceosome, across each intron. A critical step during spliceosome assembly is the recognition of the splice site sequences and branch point (BP) sequence. The BP is initially recognised by splicing factor 1 (SF1) before transfer to U2 small ribonucleoprotein (U2 snRNP). Despite its established annotation as a splicing factor, SF1’s precise function during splicing remains unclear. Recent evidence suggests that it is important for stable spliceosome association and additionally contributes to alternative splicing. Notably, SF1 pre-mRNA undergoes extensive alternative splicing in humans. This results in C-terminal sequence diversity and distinct protein motifs among SF1 protein variants. I have now identified mutations in SF1 that link its naturally occurring sequence heterogeneity (arising from alternative splicing) to the recruitment of U2 snRNP to the BP. This offers an intriguing opportunity to investigate the role of SF1 and to gain important insights into early splicing decisions. Given the substantial sequence differences and composition between SF1 protein variants, I hypothesise that SF1 variants differ in their interactome, which ultimately contributes to splicing regulation and may even contribute to the regulation of other post-transcriptional processing steps in the cell. I further hypothesize, that the contribution of SF1 variants lies in providing guidance for spliceosome assembly for subsets of introns. To test these hypotheses, we will integrate proteomic data with in vivo and in vitro protein-protein interaction measurement to disentangle SF1 variant-specific interaction networks. By combining this information with transcriptome-wide RNA binding analysis as well as data on branchpoint usage and splicing timing by SF1 variants, we aim to uncover novel principles in early spliceosome recruitment and assembly.

• DFG Programme: Research Grants