Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA.
Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA.
Nucleic Acids Res. 2023 Nov 27;51(21):11911-11926. doi: 10.1093/nar/gkad899.
Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DDR-activated APA event occurs in the first intron of CDKN1A, inducing an alternate last exon-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon DNA Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high-throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform under non-stress conditions, and SPUD is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53. The RNA binding protein HuR binds to and promotes the stability of SPUD precursor RNA. SPUD induction increases p21 protein, but not mRNA levels, affecting p21 functions in cell-cycle, CDK2 expression and cell growth. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD alters their association with CDKN1A full-length in a DDR-dependent manner, promoting CDKN1A translation. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cell-cycle.
可变聚腺苷酸化（APA）是一种动态基因表达调控的新兴机制。此前，我们描述了在 DNA 损伤反应（DDR）过程中，内含子中广泛存在 APA 事件。在这里，我们展示了一个 DDR 激活的 APA 事件发生在 CDKN1A 的第一个内含子中，诱导一个具有不同最后外显子的长非编码 RNA。我们将这个长非编码 RNA 命名为 SPUD（DNA 损伤时的选择性聚腺苷酸化）。SPUD 在细胞质中定位于多核糖体上，在可用的高通量研究中可以检测到多种亚型。在非应激条件下，与全长 CDKN1A 异构体相比，SPUD 的丰度较低，并且在多种 DNA 损伤条件下，包括在癌症和正常细胞中，SPUD 都可以被诱导，部分是通过 p53 诱导的。RNA 结合蛋白 HuR 结合并促进 SPUD 前体 RNA 的稳定性。SPUD 的诱导增加了 p21 蛋白，但不增加 mRNA 水平，从而影响细胞周期中的 p21 功能、CDK2 表达和细胞生长。与全长 CDKN1A 异构体一样，SPUD 可以与两种竞争性的 p21 翻译调节剂结合，抑制剂钙网蛋白和激活剂 CUGBP1；SPUD 以 DDR 依赖的方式改变它们与全长 CDKN1A 的结合，从而促进 CDKN1A 的翻译。总之，这些结果显示了一种新的调控机制，即长非编码 RNA 在后转录水平上控制 p21 的表达，突出了 lncRNA 在 DDR 进展和细胞周期中的相关性。
