Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Nucleic Acids Res. 2012 Apr;40(7):3131-42. doi: 10.1093/nar/gkr1009. Epub 2011 Dec 2.
Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted tRNA genes. Despite their potentially important biological roles, discovery of circular RNAs has so far been mostly serendipitous. We have developed circRNA-seq, a combined experimental/computational approach that enriches for circular RNAs and allows profiling their prevalence in a whole-genome, unbiased manner. Application of this approach to the archaeon Sulfolobus solfataricus P2 revealed multiple circular transcripts, a subset of which was further validated independently. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but were also enriched with non-coding RNAs, including C/D box RNAs and RNase P, as well as circular RNAs of unknown function. Many of the identified circles were conserved in Sulfolobus acidocaldarius, further supporting their functional significance. Our results suggest that circular RNAs, and particularly circular non-coding RNAs, are more prevalent in archaea than previously recognized, and might have yet unidentified biological roles. Our study establishes a specific and sensitive approach for identification of circular RNAs using RNA-seq, and can readily be applied to other organisms.
环状 RNA 已经在所有生命领域中被描述。这些 RNA 具有多种生物学功能，包括在病毒和类病毒基因组的生命周期以及错位 tRNA 基因成熟中的作用。尽管它们具有潜在的重要生物学作用，但环状 RNA 的发现迄今为止主要是偶然的。我们开发了 circRNA-seq，这是一种组合的实验/计算方法，可富集环状 RNA，并以全基因组、无偏倚的方式对其普遍性进行分析。将这种方法应用于古菌 Sulfolobus solfataricus P2 揭示了多个环状转录本，其中一部分进一步独立验证。鉴定出的环状 RNA 包括预期的形式，如切除的 tRNA 内含子和 rRNA 加工中间体，但也富含非编码 RNA，包括 C/D 盒 RNA 和核酶 P，以及未知功能的环状 RNA。在 Sulfolobus acidocaldarius 中鉴定出的许多圆形结构都保守存在，进一步支持了它们的功能意义。我们的研究结果表明，环状 RNA，特别是环状非编码 RNA，在古菌中比以前认为的更为普遍，并且可能具有尚未确定的生物学作用。我们的研究建立了一种使用 RNA-seq 鉴定环状 RNA 的特定而敏感的方法，并且可以很容易地应用于其他生物体。
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