Lu Yunkun, Lin Kainan, Ruan Yeling, Li Junjie, Zhang Huizhen, Pan Tianyuan, Wang Qianqian, Lin Lianyu, Feng Sijie
Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
National Engineering Research Center of Innovation and Application of Minimally Invasive Instruments, Hangzhou, 310016, China.
BMC Biol. 2025 Jun 9;23(1):164. doi: 10.1186/s12915-025-02264-1.
Alternative splicing (AS) is a substantial contributor to the high complexity of transcriptomes in multicellular eukaryotes. Fast chemical reprogramming (FCR) system is an innovative approach that facilitates the rapid transition of somatic cells into induced pluripotent stem cells (iPSCs).
In this study, we used the FCR system to delve into the dynamics of AS during cell fate transition. The trajectory of FCR, as characterized by gene expression profiles, consistently aligned with that observed in AS patterns, revealing a complex interplay between AS and gene expression regulation. Additionally, we discovered that the exon exclusion events were more prevalent than the exon inclusion events, indicating a predominant mode of splicing regulation during FCR. Compared to transcription factor-induced reprogramming (TFR), FCR showed a distinct AS pattern, underscoring the unique regulatory mechanisms governing AS in each reprogramming system. Further investigation uncovered polypyrimidine tract-binding protein 3 (Ptbp3) as an important splicing factor, possibly participating in epigenetic regulation in late stage of FCR by affecting AS of epigenetic regulators. Moreover, we found an abundance of intron retention events caused by decrease in spliceosome activity, potentially contributing to the downregulation of key diapause-related genes in the middle and late stages of FCR.
This research provided a comprehensive characterization of AS during FCR, highlighting the pivotal roles of AS in regulating cell fate transitions. Our findings advanced the understanding of the molecular mechanisms governing cell fate decisions and offered new insights into the potential of FCR for regenerative medicine and therapeutic applications.
可变剪接（AS）是多细胞真核生物转录组高度复杂性的重要贡献因素。快速化学重编程（FCR）系统是一种创新方法，可促进体细胞快速转变为诱导多能干细胞（iPSC）。
在本研究中，我们使用FCR系统深入探究细胞命运转变过程中AS的动态变化。以基因表达谱为特征的FCR轨迹与AS模式中观察到的轨迹始终一致，揭示了AS与基因表达调控之间的复杂相互作用。此外，我们发现外显子排除事件比外显子包含事件更普遍，表明FCR过程中剪接调控的主要模式。与转录因子诱导的重编程（TFR）相比，FCR显示出独特的AS模式，强调了每个重编程系统中控制AS的独特调控机制。进一步研究发现多聚嘧啶序列结合蛋白3（Ptbp3）是一种重要的剪接因子，可能通过影响表观遗传调节因子的AS参与FCR后期的表观遗传调控。此外，我们发现由于剪接体活性降低导致大量内含子保留事件，这可能在FCR的中期和后期导致关键滞育相关基因的下调。
本研究全面描述了FCR过程中的AS，突出了AS在调节细胞命运转变中的关键作用。我们的发现推进了对控制细胞命运决定分子机制的理解，并为FCR在再生医学和治疗应用中的潜力提供了新的见解。
