The RNA isoform repertoire is regulated by splicing factor (SF) expression, and alterations in SF levels are associated with disease. SFs contain ultraconserved poison exon (PE) sequences that exhibit greater identity across species than nearby coding exons, but their physiological role and molecular regulation is incompletely understood. We show that PEs in serine-arginine-rich (SR) proteins, a family of 14 essential SFs, are differentially spliced during induced pluripotent stem cell (iPSC) differentiation and in tumors versus normal tissues. We uncover an extensive cross-regulatory network of SR proteins controlling their expression via alternative splicing coupled to nonsense-mediated decay. We define sequences that regulate PE inclusion and protein expression of the oncogenic SF TRA2β using an RNA-targeting CRISPR screen. We demonstrate location dependency of RS domain activity on regulation of TRA2β-PE using CRISPR artificial SFs. Finally, we develop splice-switching antisense oligonucleotides to reverse the increased skipping of TRA2β-PE detected in breast tumors, altering breast cancer cell viability, proliferation, and migration.

RNA 亚型库受剪接因子 (SF) 表达的调节，并且 SF 水平的改变与疾病相关。 SF 含有超保守的毒外显子 (PE) 序列，与附近的编码外显子相比，该序列在物种间表现出更大的一致性，但其生理作用和分子调控尚不完全清楚。我们发现，富含丝氨酸-精氨酸（SR）蛋白（14种必需SF家族）中的PE在诱导多能干细胞（iPSC）分化过程中以及在肿瘤与正常组织中存在差异性剪接。我们发现了 SR 蛋白的广泛交叉调控网络，通过与无义介导的衰变耦合的选择性剪接来控制其表达。我们使用 RNA 靶向 CRISPR 筛选来定义调节致癌 SF TRA2β 的 PE 包含和蛋白质表达的序列。我们使用 CRISPR 人工 SF 证明了 RS 结构域活性对TRA2β - PE调节的位置依赖性。最后，我们开发了剪接转换反义寡核苷酸来逆转乳腺肿瘤中检测到的TRA2β - PE跳跃增加，从而改变乳腺癌细胞的活力、增殖和迁移。