RNA-Dependent RNA Polymerase encoding Artifacts in Eukaryotic Transcriptomes
RNA-Dependent RNA Polymerase encoding Artifacts in Eukaryotic Transcriptomes
复制标题
真核转录组中 RNA 依赖性 RNA 聚合酶编码产物
DOI：
10.16966/2471-4968.108
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发表时间：
2017
影响因子：
2.6
通讯作者：
S. Winters
中科院分区：
文献类型：
--
作者：
S. Winters
使用来自Genbank的BLAST验证的mRNA进行真核转录组的分析。每个mRNA转录物用简单的ORF查找器进行遍历，其中正向读段上有三个框传递，反向互补读段上有三个框传递。在这样做的过程中，我们达到了真核核酸（转录组）序列的编码拓扑结构分析，其与原核核酸（dsDNA基因组）序列的先前分析（在补充中总结）平行。原核基因组的反向框传递是必要的，因为序列信息仅是参考ssDNA链，需要第二个三向框传递用于完成实际dsDNA原核基因组的反向互补ssDNA。当对真核转录物也进行反向框传递时，可以看到重叠编码拓扑结构，就像在无内含子的原核基因组中看到的那样。即使真核转录物中的反义重叠编码完全无功能，它也表明无内含子的古细菌/原核生物进化人工产物与病毒真核发生假说一致（在补充材料中总结）。在讨论中，一些真核生物的反向补体转录本编码被认为是功能性的，因为它们的miRNA信号传导区域很长，这表明真核生物中RNA依赖性RNA聚合酶可能具有非RNAi作用。
Analysis of eukaryotic transcriptomes is done using BLAST validated mRNAs from Genbank. Each mRNA transcript is traversed with a simple ORF finder with three frame passes on forward reads and three frame passes on reverse compliment reads. In doing so we arrive at an encoding overlap-topology analysis of eukaryotic nucleic acid (transcriptome) sequences that parallels a previous analysis of prokaryotic nucleic acid (dsDNA genome) sequence (summarized in the Supplement). A reverse frame pass for the prokaryotic genome was necessary because the sequence information is only the reference ssDNA strand, requiring a second three-way frame pass for the reverse compliment ssDNA that completes the actual dsDNA prokaryotic genome. When the reverse frame pass is also done for the eukaryotic transcripts there is seen an overlap encoding topology like that seen in the intron-less prokaryotic genome. Even if the antisense overlap encoding in the eukaryotic transcripts is entirely non-functional, it indicates an intron-less archaeon/prokaryotic evolutionary artifact consistent with the viral eukaryogenesis hypothesis (summarized in the Supplement). In the Discussion, some of the eukaryotic reverse complement transcript encodings are thought to be functional given their lengthy miRNA signaling regions, suggesting a possible non-RNAi role for RNA-dependent RNA polymerase in eukaryotes.
影响因子：
4.5
作者：
Hale, Caryn;Kleppe, Kyle;Terns, Michael P.
通讯作者：
Terns, Michael P.
DOI：
10.1073/pnas.0503836102
发表时间：
2005-08-09
影响因子：
11.1
作者：
Shaheen, HH;Hopper, AK
通讯作者：
Hopper, AK