Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data
Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data
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DOI：
10.1007/s00436-014-3765-4
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发表时间：
2014-04-01
影响因子：
2
通讯作者：
Wu, Zhongdao
中科院分区：
文献类型：
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作者：
Liao, Qi;Shen, Jia;Wu, Zhongdao
恶性疟原虫的生命周期非常复杂，具有红细胞期，其涉及红细胞的侵入以及寄生虫在宿主内的存活和生长。在过去的几十年里，大量的研究表明，恶性疟原虫输出到感染红细胞表面的蛋白质在识别和与宿主受体相互作用中起着关键作用，因此对于恶性疟原虫生命周期的完成至关重要。然而，人们对长链非编码RNA（lncRNA）知之甚少。在这项研究中，我们设计了一个计算管道，以确定新的恶性疟原虫lncRNA从已发表的RNA-seq数据，并分析其序列和表达特征。结果发现164个新的lncRNA，其序列和表达特征与人和小鼠的lncRNA相似：缺乏序列保守性，表达水平低，与基因组中邻近编码序列的表达变异系数和共表达系数高。接下来，构建了恶性疟原虫编码/非编码基因共表达网络，以进一步注释新的和已知的lncRNA的功能。共注释了69个lncRNA的功能，其中包括44个新的lncRNA。lncRNA的主要功能包括代谢过程、生物合成过程、生物过程的调节、定位的建立、分解代谢过程、细胞组分组织以及生物体之间的种间相互作用。本研究结果将为进一步研究恶性疟原虫与宿主的相互作用及感染机制提供线索。
The life cycle of Plasmodium falciparum is very complex, with an erythrocytic stage that involves the invasion of red blood cells and the survival and growth of the parasite within the host. Over the past several decades, numbers of studies have shown that proteins exported by P. falciparum to the surface of infected red blood cells play a critical role in recognition and interaction with host receptors and are thus essential for the completion of the life cycle of P. falciparum. However, little is known about long noncoding RNAs (lncRNAs). In this study, we designed a computational pipeline to identify new lncRNAs of P. falciparum from published RNA-seq data and analyzed their sequences and expression features. As a result, 164 novel lncRNAs were found. The sequences and expression features of P. falciparum lncRNAs were similar to those of humans and mice: there was a lack of sequence conservation, low expression levels, and high expression coefficient of variance and co-expression with nearby coding sequences in the genome. Next, a coding/noncoding gene co-expression network for P. falciparum was constructed to further annotate the functions of novel and known lncRNAs. In total, the functions of 69 lncRNAs, including 44 novel lncRNAs, were annotated. The main functions of the lncRNAs included metabolic processes, biosynthetic processes, regulation of biological processes, establishment of localization, catabolic processes, cellular component organization, and interspecies interactions between organisms. Our results will provide clues to further the investigation of interactions between human hosts and parasites and the mechanisms of P. falciparum infection.