Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA.
Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
Cells. 2023 Apr 14;12(8):1160. doi: 10.3390/cells12081160.
Circular RNAs (circRNAs) are a recently discovered class of RNAs derived from protein-coding genes that have important biological and pathological roles. They are formed through backsplicing during co-transcriptional alternative splicing; however, the unified mechanism that accounts for backsplicing decisions remains unclear. Factors that regulate the transcriptional timing and spatial organization of pre-mRNA, including RNAPII kinetics, the availability of splicing factors, and features of gene architecture, have been shown to influence backsplicing decisions. Poly (ADP-ribose) polymerase I (PARP1) regulates alternative splicing through both its presence on chromatin as well as its PARylation activity. However, no studies have investigated PARP1's possible role in regulating circRNA biogenesis. Here, we hypothesized that PARP1's role in splicing extends to circRNA biogenesis. Our results identify many unique circRNAs in PARP1 depletion and PARylation-inhibited conditions compared to the wild type. We found that while all genes producing circRNAs share gene architecture features common to circRNA host genes, genes producing circRNAs in PARP1 knockdown conditions had longer upstream introns than downstream introns, whereas flanking introns in wild type host genes were symmetrical. Interestingly, we found that the behavior of PARP1 in regulating RNAPII pausing is distinct between these two classes of host genes. We conclude that the PARP1 pausing of RNAPII works within the context of gene architecture to regulate transcriptional kinetics, and therefore circRNA biogenesis. Furthermore, this regulation of PARP1 within host genes acts to fine tune their transcriptional output with implications in gene function.
环状 RNA（circRNA）是一类新发现的 RNA，来源于蛋白编码基因，具有重要的生物学和病理学作用。它们通过共转录的选择性剪接过程中的反式剪接形成；然而，负责反式剪接决策的统一机制尚不清楚。调节前体 mRNA 转录时间和空间组织的因素，包括 RNA 聚合酶 II 动力学、剪接因子的可用性以及基因结构特征，已被证明会影响反式剪接决策。多聚（ADP-核糖）聚合酶 1（PARP1）通过其在染色质上的存在及其 PAR 化活性来调节选择性剪接。然而，尚无研究探讨 PARP1 调节 circRNA 生物发生的可能作用。在这里，我们假设 PARP1 在剪接中的作用扩展到 circRNA 生物发生。我们的结果表明，与野生型相比，在 PARP1 耗尽和 PAR 化抑制条件下，会产生许多独特的 circRNA。我们发现，虽然所有产生 circRNA 的基因都具有 circRNA 宿主基因共有的基因结构特征，但在 PARP1 敲低条件下产生 circRNA 的基因的上游内含子比下游内含子长，而在野生型宿主基因中侧翼内含子是对称的。有趣的是，我们发现 PARP1 调节 RNA 聚合酶 II 暂停的行为在这两类宿主基因之间是不同的。我们得出结论，PARP1 对 RNA 聚合酶 II 暂停的调节是在基因结构的背景下进行的，以调节转录动力学，从而调节 circRNA 生物发生。此外，宿主基因内 PARP1 的这种调节作用可以精细调节其转录输出，从而影响基因功能。
