High throughput sequencing revolution reveals conserved fundamentals of U-indel editing.
High throughput sequencing revolution reveals conserved fundamentals of U-indel editing.
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高通量测序革命揭示了 U-indel 编辑的保守基础。
DOI：
10.1002/wrna.1487
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发表时间：
2018
期刊：
影响因子：
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通讯作者：
Read,LaurieK
中科院分区：
文献类型：
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作者：
Zimmer,SaraL;Simpson,RachelM;Read,LaurieK
在裸藻动物中，线粒体RNA编辑发生在双酰胺和包括寄生锥虫的动质体中。然而，U-indel编辑，其中mRNA上的开放阅读框（ORF）是通过在指导RNA指定的位置插入和删除尿苷酸而产生的，似乎仅限于动质体。多年来，指导RNA和编辑的mRNA群体的性质已经在数量惊人的物种中粗略地探索，尽管大多数动质体基因组的完整编辑的mRNA组在很大程度上缺失。然而，现在，高通量测序技术已经对我们所知道的产生了巨大的影响，并将了解U-indel编辑的机制，益处和最终编辑的产品。包括PARRS、TREAT和T-Aligner在内的工具用于组织和理解U-indel mRNA转录组，这些转录组由含有与可翻译产物一致和不一致的尿苷酸indel的mRNA组成。从高通量测序数据中得出的论点是，含有非规范编辑的“连接区”的部分编辑的mRNA是编辑中间体，相反，它们是死端产物。这些数据还显示，完全或部分编辑的给定转录物群体的百分比在转录物和生物体之间差异很大。正在解决的突出问题包括明显编码替代ORF的序列的流行，ORF末端和5′和3′非翻译区的编辑事件的多样性，以及物种之间存在的拜占庭过程的差异。高通量测序技术无疑也将被用来探测U-indel编辑的进化起源。这篇文章分类下：RNA加工> RNA编辑和修饰RNA进化和基因组学> RNA的计算分析
Among Euglenozoans, mitochondrial RNA editing occurs in the diplonemids and in the kinetoplastids that include parasitic trypanosomes. Yet U‐indel editing, in which open reading frames (ORFs) on mRNAs are generated by insertion and deletion of uridylates in locations dictated by guide RNAs, appears confined to kinetoplastids. The nature of guide RNA and edited mRNA populations has been cursorily explored in a surprisingly extensive number of species over the years, although complete sets of fully edited mRNAs for most kinetoplast genomes are largely missing. Now, however, high throughput sequencing technologies have had an enormous impact on what we know and will learn about the mechanisms, benefits, and final edited products of U‐indel editing. Tools including PARERS, TREAT, andT‐Alignerfunction to organize and make sense of U‐indel mRNA transcriptomes, which are comprised of mRNAs harboring uridylate indels both consistent and inconsistent with translatable products. From high throughput sequencing data come arguments that partially edited mRNAs containing “junction regions” of noncanonical editing are editing intermediates, and conversely, arguments that they are dead‐end products. These data have also revealed that the percent of a given transcript population that is fully or partially edited varies dramatically between transcripts and organisms. Outstanding questions that are being addressed include the prevalence of sequences that apparently encode alternative ORFs, diversity of editing events in ORF termini and 5′ and 3′ untranslated regions, and the differences that exist in this byzantine process between species. High throughput sequencing technologies will also undoubtedly be harnessed to probe U‐indel editing's evolutionary origins.This article is categorized under:RNA Processing > RNA Editing and ModificationRNA Evolution and Genomics > Computational Analyses of RNA