The regulatory role of Malat1 on the alternative splicing factor SRSF1 during CD4+ T cell differentiation

The proper activation and subsequent differentiation of naïve CD4+ T cells into effector T helper and regulatory T cells is vital for directing an appropriate adaptive immune response to specific infections. Recent evidence has identified long non-coding RNAs as novel regulators of CD4+ T cell activation and differentiation. Work by the Lagos group and others has identified the long non-coding RNA Metastasis associated lung adenocarcinoma transcript 1 (Malat1) as a critical regulator of Th cell function and immune response to chronic infection in mice. However, the mechanism behind this regulation by Malat1 is not yet fully understood. This project aimed to investigate the RNA binding protein and splicing factor SRSF1, a known Malat1 binding partner and prominent regulator of gene expression and alternative splicing in the immune system, as a mediator for Malat1 regulation of Th cell function. Through analysis of individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we have shown that SRSF1 displays alternative RNA binding behaviour in Th2 cells upon Malat1 loss. This alternative binding is directed towards RNA transcripts involved in T cell activation and differentiation, including Il2ra and Runx3. Following this, we found that Runx3 abundance is reduced and isoform usage is altered upon Malat1 loss in Th2 cells. To complement studies within Malat1-/- CD4+ T cells we attempted to develop Srsf1-/- CD4+ T cell models. Attempts to develop Srsf1-/- EL4 cell lines using CRISPR- Cas9-editing caused just a transient knockdown of SRSF1 expression, suggesting SRSF1 is essential for viability in this mouse T cell lymphoma cell line. Initial studies for establishing CRISPR-Cas9 RNP transfection into in vitro primary CD4+ T cell activation assays were unsuccessful at producing an SRSF1 knockout but have laid a foundation for further optimisation. Overall, our results identified Malat1 regulation of SRSF1 mediated RNA interaction during the Th2 cell differentiation, which serves as a promising mechanism for further investigation to better characterise Malat1 regulation of Th cell phenotype and cytokine expression.