A compendium of conserved cleavage and polyadenylation events in mammalian genes

Cleavage and polyadenylation is essential for 3’ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3’UTRs and/or coding sequences. Here we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on ~1.2 billion 3’ end sequencing reads from over 360 human, mouse and rat samples. We show that ~80% of mammalian mRNA genes contain at least one conserved PAS, and ~50% have conserved APA events. PAS conservation generally reduces promiscuous 3’ end processing, stabling gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with APA events. While tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. We show enrichment of mRNA destabilizing motifs in alternative 3’UTR sequences, leading to substantial differences in mRNA stability between 3’UTR APA isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Mutations of the U-rich motif around the PAS often accompany APA profile changes between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation involving evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic understanding of APA functions.剪切与多聚腺苷酸化（Cleavage and polyadenylation）是几乎所有真核mRNA 3'端加工过程的必需环节。近期研究表明，广泛存在的可变剪切与多聚腺苷酸化（Alternative Cleavage and Polyadenylation, APA）事件会产生携带不同3'非翻译区（3' Untranslated Region, 3'UTR）和/或编码序列的mRNA异构体。本研究基于人类、小鼠和大鼠共360余份样本的约12亿条3'端测序读段，构建了哺乳动物基因中保守型剪切与多聚腺苷酸化位点（Cleavage and Polyadenylation Sites, PASs）的整合数据集。研究显示，约80%的哺乳动物mRNA基因至少拥有一个保守型PAS，约50%的基因存在保守型APA事件。PAS的保守性通常会减少杂乱的3'端加工过程，维持跨物种间基因表达水平的稳定性。APA的保守性与基因进化年龄、基因表达特征及基因功能密切相关。具备特定功能的基因——如细胞形态维持、细胞增殖及mRNA代谢相关基因——尤其富集APA事件。尽管组织特异性基因的APA发生率通常较低，但脑特异性基因往往会演化出APA事件。本研究发现，可变3'UTR序列中富集了mRNA不稳定基序，这使得不同3'UTR型APA异构体的mRNA稳定性存在显著差异。借助保守型PAS，本研究揭示了APA位点周围的序列基序，以及剪切位点处腺苷酸的偏好性。PAS周围的富U基序发生突变，往往伴随跨物种间APA特征谱的改变。对长链非编码RNA（Long Non-Coding RNA, lncRNA）PAS的分析表明，PAS的固定机制涉及富A基序的演化。综上，本研究结果全面阐释了哺乳动物PAS的演化历程，并从系统发育角度解析了APA的功能。