MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom.
Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia.
Genome Res. 2022 May;32(5):956-967. doi: 10.1101/gr.275900.121. Epub 2022 Mar 24.
RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding RNA dimerization has been hampered by the lack of systematic in vivo detection methods. Here, we show that CLASH, PARIS, and other RNA proximity ligation methods detect RNA homodimers transcriptome-wide as "overlapping" chimeric reads that contain more than one copy of the same sequence. Analyzing published proximity ligation data sets, we show that RNA:RNA homodimers mediated by direct base-pairing are rare across the human transcriptome, but highly enriched in specific transcripts, including snoRNA, snRNA, and a subset of tRNAs. Mutations in the homodimerization domain of snoRNA impede dimerization in vitro and disrupt zebrafish development in vivo, suggesting an evolutionarily conserved role of this domain. Analysis of virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of gene in SARS-CoV-2 and gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.
RNA 同源二聚化对于各种生理过程很重要，包括无膜细胞器的组装、RNA 亚细胞定位和病毒基因组的包装。然而，由于缺乏系统的体内检测方法，RNA 二聚化的研究受到了阻碍。在这里，我们展示了 CLASH、PARIS 和其他 RNA 邻近连接方法可以在全转录组范围内检测 RNA 同源二聚体，作为包含同一序列多个拷贝的“重叠”嵌合读取。分析已发表的邻近连接数据集，我们表明，通过直接碱基配对介导的 RNA:RNA 同源二聚体在人类转录组中非常罕见，但在特定转录本中高度富集，包括 snoRNA、snRNA 和一部分 tRNA。 snoRNA 同源二聚化结构域中的突变会阻碍体外二聚化，并在体内破坏斑马鱼的发育，这表明该结构域具有进化保守的作用。对感染病毒的细胞进行分析表明，SARS-CoV-2 和 Zika 基因组的同源二聚化是由位于 SARS-CoV-2 基因和 Zika 基因蛋白编码区内特定回文序列介导的。我们推测，涉及同源二聚化的病毒基因组区域可能成为抗病毒治疗的有效靶点。
