Discovery of replicating circular RNAs by RNA-seq and computational algorithms.
Discovery of replicating circular RNAs by RNA-seq and computational algorithms.
复制标题
通过 RNA-Seq 和计算算法发现复制性环状 RNA
DOI：
10.1371/journal.ppat.1004553
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发表时间：
2014-12
期刊：
影响因子：
6.7
通讯作者：
Wu Q
中科院分区：
文献类型：
--
作者：
Zhang Z;Qi S;Tang N;Zhang X;Chen S;Zhu P;Ma L;Cheng J;Xu Y;Lu M;Wang H;Ding SW;Li S;Wu Q
复制的环状RNA是被称为类病毒的独立的植物病原体，或作为其卫星RNA调节动植物病毒的发病。在过去的40年里，这些亚病毒病原体的发现率很低，因为传统的方法技术要求高，耗时长。我们以前描述了一种不依赖同源性的发现复制环状RNA的方法，方法是使用一种称为重叠小RNA渐进过滤(PFOR)的计算程序来分析疾病组织样本中的总小RNA群体。然而，用Perl语言编写的PFOR速度非常慢，无法发现那些不会引发广泛重叠的小RNA在体内积累的亚病毒病原体。此外，PFOR尚未确定能够引发独立感染的新类病毒。本文报告了采用C++语言并行编程的PFOR2的开发，其速度是PFOR的3到8倍。进一步开发了一个新的计算程序并将其合并到PFOR2中，以允许通过对长RNA而不是小RNA进行深度测序来识别环状RNA。对葡萄和苹果植株的小RNA文库进行PFOR2分析，分别发现了葡萄潜伏类病毒(GLVd)和苹果锤头类病毒(AHVd-like RNA)。GLVd被认为是拟步甲属的一个新种，因为它含有在这组类病毒中发现的典型结构元件，并启动了对葡萄幼苗的独立侵染。AHVd-like RNA在两极都编码了一个具有生物活性的锤头状核酶，与在苹果植物中发现的任何病毒都没有特定的联系。我们认为，这些计算算法有可能在植物、无脊椎动物和脊椎动物中发现新的环状RNA，无论它们是否复制和/或诱导小RNA在体内积累。
Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of replicating circular RNAs by analysing the total small RNA populations from samples of diseased tissues with a computational program known as progressive filtering of overlapping small RNAs (PFOR). However, PFOR written in PERL language is extremely slow and is unable to discover those subviral pathogens that do not trigger in vivo accumulation of extensively overlapping small RNAs. Moreover, PFOR is yet to identify a new viroid capable of initiating independent infection. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was 3 to 8 times faster than PFOR. A new computational program was further developed and incorporated into PFOR2 to allow the identification of circular RNAs by deep sequencing of long RNAs instead of small RNAs. PFOR2 analysis of the small RNA libraries from grapevine and apple plants led to the discovery of Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA (AHVd-like RNA), respectively. GLVd was proposed as a new species in the genus Apscaviroid, because it contained the typical structural elements found in this group of viroids and initiated independent infection in grapevine seedlings. AHVd-like RNA encoded a biologically active hammerhead ribozyme in both polarities, and was not specifically associated with any of the viruses found in apple plants. We propose that these computational algorithms have the potential to discover novel circular RNAs in plants, invertebrates and vertebrates regardless of whether they replicate and/or induce the in vivo accumulation of small RNAs.