Department of Embryology, Carnegie Institution for Science, Baltimore, MD.
Mol Biol Evol. 2020 Jan 1;37(1):149-166. doi: 10.1093/molbev/msz209.
Small nucleolar RNAs (snoRNAs) function primarily as guide RNAs for posttranscriptional modification of rRNAs and spliceosomal snRNAs, both of which are functionally important and evolutionarily conserved molecules. It is commonly believed that snoRNAs and the modifications they mediate are highly conserved across species. However, most relevant data on snoRNA annotation and RNA modification are limited to studies on human and yeast. Here, we used RNA-sequencing data from the giant oocyte nucleus of the frog Xenopus tropicalis to annotate a nearly complete set of snoRNAs. We compared the frog data with snoRNA sets from human and other vertebrate genomes, including mammals, birds, reptiles, and fish. We identified many Xenopus-specific (or nonhuman) snoRNAs and Xenopus-specific domains in snoRNAs from conserved RNA families. We predicted that some of these nonhuman snoRNAs and domains mediate modifications at unexpected positions in rRNAs and snRNAs. These modifications were mapped as predicted when RNA modification assays were applied to RNA from nine vertebrate species: frogs X. tropicalis and X. laevis, newt Notophthalmus viridescens, axolotl Ambystoma mexicanum, whiptail lizard Aspidoscelis neomexicana, zebrafish Danio rerio, chicken, mouse, and human. This analysis revealed that only a subset of RNA modifications is evolutionarily conserved and that modification patterns may vary even between closely related species. We speculate that each functional domain in snoRNAs (half of an snoRNA) may evolve independently and shuffle between different snoRNAs.
小核仁 RNA（snoRNAs）主要作为 rRNA 和剪接体 snRNA 转录后修饰的指导 RNA，这两种 RNA 都具有重要的功能和高度保守的进化特征。人们普遍认为 snoRNAs 及其介导的修饰在物种间高度保守。然而，关于 snoRNA 注释和 RNA 修饰的大多数相关数据仅限于人类和酵母的研究。在这里，我们使用来自青蛙 Xenopus tropicalis 的巨大卵细胞核的 RNA-seq 数据来注释几乎完整的 snoRNA 集。我们将青蛙数据与来自人类和其他脊椎动物基因组（包括哺乳动物、鸟类、爬行动物和鱼类）的 snoRNA 集进行了比较。我们鉴定了许多 Xenopus 特异性（或非人类） snoRNAs 和 snoRNA 保守家族中的 snoRNAs 特异性结构域。我们预测，这些非人类 snoRNAs 和结构域中的一些介导 rRNA 和 snRNA 中意想不到位置的修饰。当将 RNA 修饰测定应用于来自九个脊椎动物物种的 RNA 时，预测了这些修饰：青蛙 Xenopus tropicalis 和 Xenopus laevis、蝾螈 Notophthalmus viridescens、墨西哥钝口螈 Ambystoma mexicanum、鞭尾蜥 Aspidoscelis neomexicana、斑马鱼 Danio rerio、鸡、鼠和人。该分析表明，只有一小部分 RNA 修饰是进化保守的，修饰模式甚至在亲缘关系密切的物种之间也可能存在差异。我们推测 snoRNAs 中的每个功能结构域（snoRNA 的一半）可能独立进化，并在不同的 snoRNAs 之间重新组合。
