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3'READS+RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association
RNA ( IF 4.5 ) Pub Date : 2020-08-12 , DOI: 10.1261/rna.076133.120
Dinghai Zheng , Hana Cho , Wei Wang , Xavier Rambout , Bin Tian , Lynne E. Maquat

Staufen1 (STAU1) is an RNA-binding protein (RBP) that interacts with double-stranded RNA structures and has been implicated in regulating different aspects of mRNA metabolism. Previous studies have indicated that STAU1 interacts extensively with RNA structures in coding regions (CDSs) and 3'-untranslated regions (3'UTRs). In particular, duplex structures formed within 3'UTRs by inverted-repeat Alu elements (IRAlus) interact with STAU1 through its double-stranded RNA-binding domains (dsRBDs). Using 3' region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3'READS+RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3'UTRs. Overall, relative to short 3'UTR counterparts, longer 3'UTR isoforms of genes have stronger STAU1 binding, most likely due to a higher frequency of RNA structures, including particular IRAlus. Nevertheless, a sizable fraction of genes express transcripts showing the opposite trend, attributable to AU-rich sequences in their alternative 3'UTRs, possibly recruiting antagonistic RBPs and/or destabilizing STAU1-binding RNA structures. Using STAU1-knockout cells, we show that strong STAU1 binding to mRNA 3'UTRs generally enhances polysome association. However, IRAlus have little impact on STAU1-mediated polysome association despite having strong interactions with the protein.Taken together, our work reveals complex interactions of STAU1 with its cognate RNA substrates. Our data also shed important light on diversity in co- and post-transcriptional regulation for the widespread APA isoforms in mammalian cells.

中文翻译:

3'READS+RIP 定义了不同的 Staufen1 与替代 3'UTR 亚型的结合,并揭示了影响结合和多聚体结合的结构和序列基序

Staufen1 (STAU1) 是一种 RNA 结合蛋白 (RBP),可与双链 RNA 结构相互作用,并参与调节 mRNA 代谢的不同方面。以前的研究表明,STAU1 与编码区 (CDS) 和 3'-非翻译区 (3'UTR) 中的 RNA 结构广泛相互作用。特别是,由反向重复 Alu 元件 (IRAlus) 在 3'UTR 内形成的双链结构通过其双链 RNA 结合域 (dsRBD) 与 STAU1 相互作用。使用 3' 区域提取和深度测序与核糖核蛋白免疫沉淀 (3'READS+RIP) 结合,再加上重新分析以前的 STAU1 结合和 RNA 结构数据,我们描绘了转录组范围内的 STAU1 相互作用,包括替代多聚腺苷酸化 (APA) 亚型之间的结合差异。与之前的报告一致,RNA 结构是 STAU1 与 CDS 和 3'UTR 结合的主要特征。总体而言,相对于较短的 3'UTR 对应物,较长的 3'UTR 基因同种型具有更强的 STAU1 结合,这很可能是由于更高频率的 RNA 结构,包括特定的 IRAlus。然而,相当一部分基因表达的转录本显示出相反的趋势,这归因于其替代 3'UTR 中富含 AU 的序列,可能会招募拮抗性 RBP 和/或破坏 STAU1 结合 RNA 结构。使用 STAU1 基因敲除细胞,我们表明 STAU1 与 mRNA 3'UTR 的强结合通常会增强 polysome 关联。然而,尽管 IRAlus 与蛋白质有很强的相互作用,但它对 STAU1 介导的多核糖体关联几乎没有影响。我们的工作揭示了 STAU1 与其同源 RNA 底物的复杂相互作用。我们的数据还为哺乳动物细胞中广泛的 APA 亚型的共转录和转录后调控的多样性提供了重要启示。
更新日期:2020-08-12
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