SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells [RNA-seq]

SF3B1, a critical component of the U2 snRNP splicing factor, is frequently mutated in cancer and plays a crucial role in pre-mRNA splicing. We investigated the effects of the most common SF3B1 mutation, heterozygous substitution of Lysine 700 to Glutamate (K700E), in human embryonic stem (hESC) cells using CRISPR-Cas9 to generate heterozygous SF3B1K700E clones. We observed the upregulation of several key transcription regulators associated with hematopoiesis and a broad range of immune genes in SF3B1K700E hESCs. Despite transcriptional differences between hESC and myelodysplastic syndrome (MDS) cells harboring the SF3B1K700E mutation, several common gene programs were identified in both cell types, independent of splicing alterations. To further elucidate the molecular mechanisms underlying dysregulated gene expression in SF3B1K700E hESCs, we performed Precision Run-On sequencing (PRO-seq) in SF3B1K700E hESCs. These analyses revealed alterations in RNA polymerase II (Pol II) elongation properties induced by the SF3B1K700E mutation. Specifically, a general increase in pause release was noted in SF3B1K700E hESCs. This study identifies several downstream candidate genes that could contribute to the SF3B1 mutated phenotype, shedding light on the impact of the U2 snRNP on transcription by Pol II.