Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers
Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers
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DOI：
10.1038/s41598-019-55573-1
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发表时间：
2019-12-20
影响因子：
4.6
通讯作者：
Telford, Maximilian J.
中科院分区：
文献类型：
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作者：
Natsidis, Paschalis;Schiffer, Philipp H.;Telford, Maximilian J.
在一些真核生物中，“隐藏断裂”被描述为 28S 核糖体 RNA 分子被切割成两个子部分。这种断裂在原口动物（节肢动物、软体动物、环节动物等）中很常见，但在一些脊椎动物和非后生动物真核生物中也有报道称断裂。我们提出了一种新的计算方法，使用 RNA-Seq 数据作图来确定 28S rRNA 中隐藏断裂的存在。我们发现原口动物中存在同源断裂，尽管它在少数类群中丢失了。我们发现脊椎动物 28S rRNA 中的罕见断裂与原口断裂并不同源。在所研究的 331 个非动物真核生物物种中，仅在 4 个物种中发现了断裂，其中三个断裂与原口断裂位于同一位置，这表明这是趋同进化的惊人实例。 RNA 完整性值 (RIN) 依赖于完整的 28S rRNA，并且在大多数有断裂的动物物种中将始终被低估。
In some eukaryotes, a 'hidden break' has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.), but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although it has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and, in three of these, the break is located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28S rRNA and will be consistently underestimated in the great majority of animal species with a break.