Transcriptome-wide discovery of circular RNAs in Archaea.
Transcriptome-wide discovery of circular RNAs in Archaea.
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DOI：
10.1093/nar/gkr1009
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发表时间：
2012-04
影响因子：
14.9
通讯作者：
Sorek R
中科院分区：
文献类型：
--
作者：
Danan M;Schwartz S;Edelheit S;Sorek R
在生命的各个领域都描述了环状RNA的形式。这些RNA被证明具有不同的生物学功能，包括在病毒和类病毒基因组的生命周期中的作用，以及在排列的tRNA基因的成熟中的作用。尽管它们具有潜在的重要生物学作用，但迄今为止，环状RNA的发现大多是偶然的。我们开发了circRNA-seq，这是一种结合实验/计算的方法，可以富集环状RNA，并允许以全基因组、无偏见的方式分析其患病率。这种方法的应用古菌硫磺硫化叶菌P2揭示了多个环状转录本，其中一个子集进一步独立验证。鉴定的环状RNA包括预期的形式，例如切除的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RNase P，以及功能未知的环状RNA。许多鉴定的环在酸热硫化叶菌中是保守的，进一步支持它们的功能意义。我们的研究结果表明，环状RNA，特别是环状非编码RNA，在古细菌中比以前认识到的更普遍，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的特异性和灵敏度的方法，并且可以很容易地应用于其他生物。
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.
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