Analysis of Long Non-Coding RNA in Cryptosporidium parvum Reveals Significant Stage-Specific Antisense Transcription.
Analysis of Long Non-Coding RNA in Cryptosporidium parvum Reveals Significant Stage-Specific Antisense Transcription.
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DOI：
10.3389/fcimb.2020.608298
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发表时间：
2020
影响因子：
5.7
通讯作者：
Kissinger JC
中科院分区：
文献类型：
--
作者：
Li Y;Baptista RP;Sateriale A;Striepen B;Kissinger JC
隐孢子虫是一种原生寄生虫，已被确定为两岁以下儿童中重度腹泻的第二大原因，也是全球范围内死亡的重要原因。隐孢子虫在单个宿主中有一个复杂的、专属的、胞内的、但胞质外的生命周期。这种寄生虫中的基因是如何调控的，目前在很大程度上仍不清楚。长的非编码RNA(LncRNAs)发挥着重要的调节作用，包括在广泛的生物体中的基因表达。隐孢子虫LncRNAs已被报道进入宿主细胞核并影响宿主反应。然而，还没有对隐孢子虫中的lncRNAs进行系统的研究，以确定更多的lncRNAs。在这项研究中，我们分析了微小隐孢子虫体外链特异的RNA-seq发育时间序列，涵盖了无性和有性两个阶段，以确定与寄生虫发育相关的lncRNA。我们总共识别了396个新的lncRNA，大部分是反义的，其中86%是差异表达的。令人惊讶的是，近10%的带注释的mRNA有反义转录本。LncRNAs最常出现在其相应的正义mRNA的3‘端。已确定了可能的lncRNA调节区，其中许多似乎编码双向启动子。LncRNA与上游mRNA表达呈正相关。在微小隐孢子虫、人隐翅虫和白纹伊蚊之间观察到lncRNA候选基因的进化保守性和表达。10个带有反义转录本的微小疟原虫蛋白编码基因都有恶性疟原虫的同源基因，这些基因也有反义转录本。利用RT-PCR和RT-qPCR对三个具有特殊性质(例如内含子剪接)的微小隐孢子虫LncRNAs进行了实验验证。微小隐孢子虫非编码转录组的这一初步特征有助于进一步研究lncRNAs在寄生虫发育和宿主-病原体相互作用中的作用。
Cryptosporidium is a protist parasite that has been identified as the second leading cause of moderate to severe diarrhea in children younger than two and a significant cause of mortality worldwide. Cryptosporidium has a complex, obligate, intracellular but extra cytoplasmic lifecycle in a single host. How genes are regulated in this parasite remains largely unknown. Long non-coding RNAs (lncRNAs) play critical regulatory roles, including gene expression across a broad range of organisms. Cryptosporidium lncRNAs have been reported to enter the host cell nucleus and affect the host response. However, no systematic study of lncRNAs in Cryptosporidium has been conducted to identify additional lncRNAs. In this study, we analyzed a C. parvum in vitro strand-specific RNA-seq developmental time series covering both asexual and sexual stages to identify lncRNAs associated with parasite development. In total, we identified 396 novel lncRNAs, mostly antisense, with 86% being differentially expressed. Surprisingly, nearly 10% of annotated mRNAs have an antisense transcript. lncRNAs occur most often at the 3′ end of their corresponding sense mRNA. Putative lncRNA regulatory regions were identified and many appear to encode bidirectional promoters. A positive correlation between lncRNA and upstream mRNA expression was observed. Evolutionary conservation and expression of lncRNA candidates was observed between C. parvum, C. hominis and C. baileyi. Ten C. parvum protein-encoding genes with antisense transcripts have P. falciparum orthologs that also have antisense transcripts. Three C. parvum lncRNAs with exceptional properties (e.g., intron splicing) were experimentally validated using RT-PCR and RT-qPCR. This initial characterization of the C. parvum non-coding transcriptome facilitates further investigations into the roles of lncRNAs in parasite development and host-pathogen interactions.