3′ untranslated regions (3′ UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect various aspects of the RNA life cycle including transcript stability and cellular localization. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3′ UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3′-UTR dynamics in T helper cells, we investigated division-dependent alternative polyadenylation (APA). In addition, we generated 3′ end UTR sequencing data from naive, activated, memory, and regulatory CD4+ T cells. 3′-UTR length changes were estimated using a nonnegative matrix factorization approach and were compared with those inferred from long-read PacBio sequencing. We found that APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNA-seq data set, we did not find evidence of APA association with differential gene expression or transcript usage, indicating that APA has only a marginal effect on transcript abundance. 3′-UTR sequence analysis revealed conserved binding sites for T cell-relevant microRNAs and RBPs in the alternative 3′ UTRs. These results indicate that poly(A) site usage could play an important role in the control of cell fate decisions and homeostasis.
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机译：3' 非翻译区 （3' UTR） 是信使 RNA 的关键元件，因为它们包含 RNA 结合蛋白 （RBP） 和 microRNA 的结合位点，这些位点会影响 RNA 生命周期的各个方面，包括转录本稳定性和细胞定位。为了响应 T 细胞受体激活，T 细胞在免疫反应的效应期经历大量扩增，并动态修改其 3′ UTR。这是否用于直接调节特定 mRNA 的丰度，还是增殖的次要效应尚不清楚。为了研究 T 辅助细胞中的 3′-UTR 动力学，我们研究了分裂依赖性选择性多聚腺苷酸化 （APA）。此外，我们还从初始、活化、记忆和调节 CD4+ T 细胞生成了 3' 末端 UTR 测序数据。使用非负基质分解方法估计 3′-UTR 长度变化，并与从长读长 PacBio 测序推断的变化进行比较。我们发现 APA 事件是瞬态的，并在效应子阶段扩展后恢复。使用正交的批量 RNA-seq 数据集，我们没有发现 APA 与差异基因表达或转录本使用相关的证据，这表明 APA 对转录本丰度的影响很小。3'-UTR 序列分析揭示了替代 3' UTR 中 T 细胞相关 microRNA 和 RBP 的保守结合位点。这些结果表明，poly（A） 位点的使用可能在控制细胞命运决策和体内平衡中发挥重要作用。
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