Long terminal repeat (LTR)-retrotransposons are significant contributors to the evolution and diversity of eukaryotic genomes. Their RNA genomes (gRNA) serve as a template for protein synthesis and reverse transcription to a DNA copy, which can integrate into the host genome. Here, we used the SHAPE-MaP strategy to explore Ty3 retrotransposon gRNA structure in yeast and under cell-free conditions. Our study reveals the structural dynamics of Ty3 gRNA and the well-folded core, formed independently of the cellular environment. Based on the detailed map of Ty3 gRNA structure, we characterized the structural context of cis-acting sequences involved in reverse transcription and frameshifting. We also identified a novel functional sequence as a potential initiator for Ty3 gRNA dimerization. Our data indicate that the dimer is maintained by direct interaction between short palindromic sequences at the 5′ ends of the two Ty3 gRNAs, resembling the model characteristic for other retroelements like HIV-1 and Ty1. This work points out a range of cell-dependent and -independent Ty3 gRNA structural changes that provide a solid background for studies on RNA structure-function relationships important for retroelement biology.

中文翻译：

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绘制酵母 Ty3 反转录转座子 RNA 基因组的结构图谱


长末端重复序列 （LTR） -反转录转座子是真核基因组进化和多样性的重要贡献者。它们的 RNA 基因组 （gRNA） 用作蛋白质合成和逆转录成 DNA 拷贝的模板，DNA 拷贝可以整合到宿主基因组中。在这里，我们使用 SHAPE-MaP 策略来探索酵母和无细胞条件下的 Ty3 反转录转座子 gRNA 结构。我们的研究揭示了 Ty3 gRNA 的结构动力学和独立于细胞环境形成的折叠良好的核心。基于 Ty3 gRNA 结构的详细图谱，我们表征了参与逆转录和移码的顺式作用序列的结构背景。我们还确定了一种新的功能序列作为 Ty3 gRNA 二聚化的潜在起始剂。我们的数据表明，二聚体是通过两个 Ty3 gRNA 的 5' 末端的短回文序列之间的直接相互作用来维持的，类似于 HIV-1 和 Ty1 等其他逆转录元件的模型特征。这项工作指出了一系列细胞依赖性和不依赖性的 Ty3 gRNA 结构变化，这些变化为研究对逆转录元件生物学很重要的 RNA 结构-功能关系提供了坚实的背景。