Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA.
Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
Exp Mol Med. 2024 Oct;56(10):2145-2161. doi: 10.1038/s12276-024-01289-w. Epub 2024 Oct 1.
Alternative cleavage and polyadenylation within introns (intronic APA) generate shorter mRNA isoforms; however, their physiological significance remains elusive. In this study, we developed a comprehensive workflow to analyze intronic APA profiles using the mammalian target of rapamycin (mTOR)-regulated transcriptome as a model system. Our investigation revealed two contrasting effects within the transcriptome in response to fluctuations in cellular mTOR activity: an increase in intronic APA for a subset of genes and a decrease for another subset of genes. The application of this workflow to RNA-seq data from The Cancer Genome Atlas demonstrated that this dichotomous intronic APA pattern is a consistent feature in transcriptomes across both normal tissues and various cancer types. Notably, our analyses of protein length changes resulting from intronic APA events revealed two distinct phenomena in proteome programming: a loss of functional domains due to significant changes in protein length or minimal alterations in C-terminal protein sequences within unstructured regions. Focusing on conserved intronic APA events across 10 different cancer types highlighted the prevalence of the latter cases in cancer transcriptomes, whereas the former cases were relatively enriched in normal tissue transcriptomes. These observations suggest potential, yet distinct, roles for intronic APA events during pathogenic processes and emphasize the abundance of protein isoforms with similar lengths in the cancer proteome. Furthermore, our investigation into the isoform-specific functions of JMJD6 intronic APA events supported the hypothesis that alterations in unstructured C-terminal protein regions lead to functional differences. Collectively, our findings underscore intronic APA events as a discrete molecular signature present in both normal tissues and cancer transcriptomes, highlighting the contribution of APA to the multifaceted functionality of the cancer proteome.
内含子剪接和多聚腺苷酸化（intronic APA）会产生较短的 mRNA 异构体；然而，其生理意义仍难以捉摸。在这项研究中，我们开发了一种全面的工作流程，以分析雷帕霉素（mTOR）调控转录组作为模型系统的内含子 APA 谱。我们的研究揭示了细胞 mTOR 活性波动时转录组内的两种相反效应：一部分基因的内含子 APA 增加，另一部分基因的内含子 APA 减少。将该工作流程应用于癌症基因组图谱（TCGA）的 RNA-seq 数据表明，这种二分内含子 APA 模式是正常组织和各种癌症类型转录组中的一致特征。值得注意的是，我们对内含子 APA 事件导致的蛋白质长度变化的分析揭示了蛋白质组编程中的两个不同现象：由于蛋白质长度的显著变化而导致功能域丢失，或在无结构区域内 C 端蛋白质序列的微小改变。关注 10 种不同癌症类型中保守的内含子 APA 事件，突出了后者在癌症转录组中的普遍性，而前者在正常组织转录组中相对丰富。这些观察结果表明内含子 APA 事件在致病过程中可能具有但又不同的作用，并强调了癌症蛋白质组中具有相似长度的蛋白质异构体的丰富性。此外，我们对 JMJD6 内含子 APA 事件的同工型特异性功能的研究支持了这样的假设，即无结构 C 端蛋白质区域的改变会导致功能差异。总的来说，我们的研究结果强调了内含子 APA 事件作为存在于正常组织和癌症转录组中的离散分子特征，突出了 APA 对癌症蛋白质组多方面功能的贡献。
