Suppr超能文献

PARP1 通过控制转录动力学调节环状 RNA 的生物发生。

PARP1 Regulates Circular RNA Biogenesis though Control of Transcriptional Dynamics.

机构信息

Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA.

Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.

出版信息

Cells. 2023 Apr 14;12(8):1160. doi: 10.3390/cells12081160.

Abstract

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.

摘要

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。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfed/10136798/5ec4a3b09321/cells-12-01160-g001.jpg

相似文献

1
PARP1 Regulates Circular RNA Biogenesis though Control of Transcriptional Dynamics.
Cells. 2023 Apr 14;12(8):1160. doi: 10.3390/cells12081160.
4
Exploring the interplay between PARP1 and circRNA biogenesis and function.
Wiley Interdiscip Rev RNA. 2023 Nov 13:e1823. doi: 10.1002/wrna.1823.
5
Formation of Circular RNAs.
Adv Exp Med Biol. 2025;1485:99-115. doi: 10.1007/978-981-96-9428-0_7.
6
Approach to Measuring the Effect of PARP1 on RNA Polymerase II Elongation Rates.
Methods Mol Biol. 2023;2609:315-328. doi: 10.1007/978-1-0716-2891-1_18.
7
PARP1 is a versatile factor in the regulation of mRNA stability and decay.
Sci Rep. 2019 Mar 6;9(1):3722. doi: 10.1038/s41598-019-39969-7.
9
The structural view of the protein PGD-219aa encoded by the circular RNA CircPGD.
J Mol Model. 2025 Aug 9;31(9):236. doi: 10.1007/s00894-025-06454-0.
10
Cooperative nucleic acid binding by Poly ADP-ribose polymerase 1.
Sci Rep. 2024 Mar 29;14(1):7530. doi: 10.1038/s41598-024-58076-w.

引用本文的文献

1
SELEX identifies high-affinity RNA targets for chromatin-binding proteins PARP1 and MeCP2.
iScience. 2025 Aug 6;28(9):113299. doi: 10.1016/j.isci.2025.113299. eCollection 2025 Sep 19.
2
Exploring the interplay between PARP1 and circRNA biogenesis and function.
Wiley Interdiscip Rev RNA. 2023 Nov 13:e1823. doi: 10.1002/wrna.1823.
3
Circular RNAs Variously Participate in Coronary Atherogenesis.
Curr Issues Mol Biol. 2023 Aug 13;45(8):6682-6700. doi: 10.3390/cimb45080422.
4
The dynamic process of covalent and non-covalent PARylation in the maintenance of genome integrity: a focus on PARP inhibitors.
NAR Cancer. 2023 Aug 21;5(3):zcad043. doi: 10.1093/narcan/zcad043. eCollection 2023 Sep.
5
Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures.
J Mol Biol. 2024 Jan 1;436(1):168207. doi: 10.1016/j.jmb.2023.168207. Epub 2023 Jul 20.

本文引用的文献

1
Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging.
iScience. 2022 Dec 9;26(1):105779. doi: 10.1016/j.isci.2022.105779. eCollection 2023 Jan 20.
3
4
Alternative splicing modulation by G-quadruplexes.
Nat Commun. 2022 May 3;13(1):2404. doi: 10.1038/s41467-022-30071-7.
5
Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops.
Elife. 2022 Feb 22;11:e69476. doi: 10.7554/eLife.69476.
6
Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks.
Front Genet. 2022 Jan 31;13:793884. doi: 10.3389/fgene.2022.793884. eCollection 2022.
7
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions.
Nucleic Acids Res. 2022 Jan 7;50(D1):D222-D230. doi: 10.1093/nar/gkab1079.
8
Evolutionary dynamics of circular RNAs in primates.
Elife. 2021 Sep 20;10:e69148. doi: 10.7554/eLife.69148.
9
RNA polymerase II speed: a key player in controlling and adapting transcriptome composition.
EMBO J. 2021 Aug 2;40(15):e105740. doi: 10.15252/embj.2020105740. Epub 2021 Jul 13.
10

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验