Background <p>SF3B4 encodes a core subunit of the U2-type spliceosome and is implicated in abnormal cell growth and tumorigenesis. However, its role in regulating gene expression and alternative splicing in hepatocellular carcinoma (HCC) remains inadequately understood.</p> Methods <p>SF3B4 expression was downregulated in HCC cells, followed by high-throughput transcriptome sequencing to capture the transcriptomic changes induced by SF3B4. This approach facilitated the identification of potential targets regulated by SF3B4 at both the transcriptional and alternative splicing levels in HCC cells. Additionally, SF3B4-binding RNAs in Huh7 cells were identified through iRIP-seq.&#xa0;The RNA-seq data were subsequently analyzed to elucidate the molecular mechanisms by which SF3B4 affects gene expression and alternative splicing in HCC.</p> Results <p>Downregulation of SF3B4 promoted apoptosis and inhibited cell proliferation. In the RNA-seq data, the number of regulated alternative splicing events (RASE) significantly outnumbered the differentially expressed genes (DEGs), consistent with SF3B4’s role as a splicing factor that regulates a wide array of pre-mRNA splicing events. Furthermore, a total of 252 common RNA targets bound by SF3B4 were identified. Correlation analysis with RNA-seq data suggested that SF3B4 may bind to TRIM28, potentially modulating its mRNA expression levels. Additionally, SF3B4 may influence pre-mRNA alternative splicing by interacting with SETD5.</p> Conclusion <p>SF3B4 contributes to HCC progression by directly binding mRNAs and interacting with proteins, thereby regulating gene expression and alternative splicing.</p>