Promoter R-Loops Recruit U2AF1 to Modulate Its Phase Separation and RNA Splicing,Journal of the American Chemical Society

当前位置： X-MOL 学术 › J. Am. Chem. Soc. › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Promoter R-Loops Recruit U2AF1 to Modulate Its Phase Separation and RNA Splicing
Journal of the American Chemical Society ( IF 14.4 ) Pub Date : 2023-09-21 , DOI: 10.1021/jacs.3c08204
Xiaomei He ₁ , Jun Yuan ₂ , Zi Gao ₁ , Yinsheng Wang _{1,

2}

Affiliation

R-loops and guanine quadruplexes (G4s) are secondary structures of nucleic acids that are ubiquitously present in cells and are enriched in promoter regions of genes. By employing a bioinformatic approach based on overlap analysis of transcription factor chromatin immunoprecipitation sequencing (ChIP-seq) data sets, we found that many splicing factors, including U2AF1 whose recognition of the 3′ splicing site is crucial for pre-mRNA splicing, exhibit pronounced enrichment at endogenous R-loop- and DNA G4-structure loci in promoter regions of human genes. We also revealed that U2AF1 binds directly to R-loops and DNA G4 structures at a low-nM binding affinity. Additionally, we showed the ability of U2AF1 to undergo phase separation, which could be stimulated by binding with R-loops, but not duplex DNA, RNA/DNA hybrid, DNA G4, or single-stranded RNA. We also demonstrated that U2AF1 binds to promoter R-loops in human cells, and this binding competes with U2AF1’s interaction with 3′ splicing site and leads to augmented distribution of RNA polymerase II (RNAPII) to promoters over gene bodies, thereby modulating cotranscriptional pre-mRNA splicing. Together, we uncovered a group of candidate proteins that can bind to both R-loops and DNA G4s, revealed the direct and strong interactions of U2AF1 with these nucleic acid structures, and established a biochemical rationale for U2AF1’s occupancy in gene promoters. We also unveiled that interaction with R-loops promotes U2AF1’s phase separation, and our work suggests that U2AF1 modulates pre-mRNA splicing by regulating RNAPII’s partition in transcription initiation versus elongation.

中文翻译：

启动子 R 环招募 U2AF1 来调节其相分离和 RNA 剪接

R 环和鸟嘌呤四链体 (G4) 是细胞中普遍存在的核酸二级结构，并且富含于基因的启动子区域。通过采用基于转录因子染色质免疫沉淀测序 (ChIP-seq) 数据集重叠分析的生物信息学方法，我们发现许多剪接因子，包括 U2AF1，其对 3' 剪接位点的识别对于前 mRNA 剪接至关重要。人类基因启动子区域内源性 R 环和 DNA G4 结构位点的富集。我们还发现 U2AF1 以低 nM 的结合亲和力直接与 R 环和 DNA G4 结构结合。此外，我们还展示了 U2AF1 进行相分离的能力，这种能力可以通过与 R 环结合来刺激，但不能通过与双链 DNA、RNA/DNA 杂交体、DNA G4 或单链 RNA 结合来刺激。我们还证明，U2AF1 与人类细胞中的启动子 R 环结合，这种结合与 U2AF1 与 3' 剪接位点的相互作用竞争，导致 RNA 聚合酶 II (RNAPII) 在基因体上向启动子的分布增加，从而调节共转录前mRNA 剪接。我们共同发现了一组可以与 R 环和 DNA G4 结合的候选蛋白，揭示了 U2AF1 与这些核酸结构的直接而强烈的相互作用，并建立了 U2AF1 在基因启动子中占据的生化原理。我们还揭示了与 R 环的相互作用促进 U2AF1 的相分离，并且我们的工作表明 U2AF1 通过调节 RNAPII 在转录起始与延伸中的分配来调节前 mRNA 剪接。

更新日期：2023-09-21

点击分享查看原文

点击收藏

公开下载

阅读更多本刊新发论文本刊介绍/投稿指南