Data from: Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD. We show that evolutionary progression of 3' splice sites is coupled with longer repressive uridine tracts. Once the 3' splice site at ancient Alu-exons reaches a stable phase, splicing repression by hnRNPC decreases, but the exons generally remain sensitive to NMD. We conclude that repressive motifs are strongest next to cryptic exons and that gradual weakening of these motifs contributes to the evolutionary emergence of new alternative exons.Alu元件（Alu elements）是一类逆转录转座子（retrotransposon），在灵长类动物的进化过程中频繁参与新外显子的形成。本研究旨在剖析异质性细胞核核糖蛋白C（hnRNPC）介导的剪接抑制与无义介导的mRNA降解（NMD）之间的协同互作，及其在新型Alu外显子（Alu-exon）的质量控制与进化进程中的作用。本研究共鉴定出3100个新型Alu外显子，并证实相较于携带提前终止密码子的其他外显子，无义介导的mRNA降解（NMD）能更高效地识别带有Alu外显子的转录本。但部分Alu外显子可逃脱NMD的监控，尤其是当相邻内含子发生滞留时，这凸显了剪接抑制与NMD协同调控的重要性。研究发现，3'剪接位点（3' splice site）的进化历程与更长的抑制性尿苷区段密切相关。当古老Alu外显子的3'剪接位点进入稳定阶段后，hnRNPC介导的剪接抑制作用会减弱，但此类外显子通常仍对NMD敏感。本研究最终得出结论：隐蔽外显子（cryptic exon）旁侧的抑制基序作用最强，而这类基序的逐步弱化，推动了新型可变外显子（alternative exon）的进化出现。