EAPP is essential for tri-snRNP biogenesis and controls cell fate and tumor growth via the alternative splicing of MDM4

Precursor messenger RNA (pre-mRNA) splicing is catalyzed by the spliceosome, a highly dynamic machinery with sequentially assembled small nuclear ribonucleoproteins (snRNPs) and splicing factors. Aberrant spliceosome composition and function result in the dysregulation of pre-mRNA alternative splicing, which may cause cellular stresses and diseases such as cancer. Here, we identify a splicing factor, E2F-associated phosphoprotein (EAPP), that directly binds to the U4/U6. U5 tri-snRNP and PRPF19 complex. Notably, the C-terminal “bucket” domain in EAPP composed of several beta-sheets is required for its interaction with the tri-snRNP. EAPP is prominently located at Cajal bodies within the nucleus where it colocalizes with the spliceosome. Loss of EAPP impedes the assembly and homeostasis of the tri-snRNP complex in Cajal bodies and increases the frequency of splicing abnormalities, mostly exon skipping. Moreover, EAPP depletion promotes MDM4 exon 6 skipping, which suppresses cell growth and tumor progression via p53 overactivation. Our study demonstrates a previously uncharacterized function of EAPP in spliceosome regulation and reveals that EAPP-mediated alternative splicing of MDM4 is a critical determinant of cell fate and tumor growth. To further investigate how EAPP affects the downstream regulatory mechanisms of tumor cell growth, we utilized CRISPR/Cas9 technology to knock out EAPP in HeLa cells. Infect cells with lentiCRISPR-Cas9 lentivirus. After 48 hours, add 2 μg/ml puromycin to select for transduced cells, and select and expand single-cell clones. We then performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression and alternative splicing profiling analysis of RNA-seq data for EAPP knockout and WT HeLa cells.