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Abstract：
Plasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent progress in sequencing techniques has made it possible to study the secondary structures of RNA molecules at the transcriptomic level. Thus, in this study we produced the in vivo RNA structurome of a protozoan parasite with a highly A/U-biased transcriptome. We showed that it is possible to probe the secondary structures of P. falciparum RNA molecules in vivo using two different chemical probes, and obtained structures for more than half of all transcripts in the transcriptome. These showed greater stability (lower free energy) than the same structures modelled in silico, and structural features appeared to influence translation efficiency and RNA decay. Finally, we compared the P. falciparum RNA structurome with the predicted RNA structurome of an A/U-balanced species, P. knowlesi, finding a bias towards lower overall transcript stability and more hairpins and multi-stem loops in P. falciparum. This unusual protozoan RNA structurome will provide a basis for similar studies in other protozoans and also in other unusual genomes.
摘要：
恶性疟原虫,一种原生动物寄生虫和人类疟疾的病原体，具有迄今为止测序的最有A/T偏见的基因组之一。这可能赋予基因组和转录组不同寻常的结构特征。测序技术的最新进展使得在转录组水平上研究RNA分子的二级结构成为可能。因此，在这项研究中，我们产生了具有高度A/U偏向转录组的原生动物寄生虫的体内RNA结构。我们表明，可以使用两种不同的化学探针在体内探测恶性疟原虫RNA分子的二级结构，并获得了转录组中一半以上转录本的结构。这些显示出更高的稳定性（较低的自由能）比相同的结构在硅模拟，结构特征似乎会影响翻译效率和RNA衰变。最后,我们将恶性疟原虫RNA结构与A/U平衡物种的预测RNA结构进行了比较，P.Knowlesi,在恶性疟原虫中发现总体转录物稳定性较低，发夹和多茎环偏倚。这种不寻常的原生动物RNA结构将为其他原生动物以及其他不寻常基因组的类似研究提供基础。
