Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis.
Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis.
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DOI：
10.1128/msphere.01061-20
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发表时间：
2021-01-06
期刊：
影响因子：
4.8
通讯作者：
Carlton JM
中科院分区：
文献类型：
--
作者：
Warring SD;Blow F;Avecilla G;Orosco JC;Sullivan SA;Carlton JM
由阴道毛滴虫引起的滴虫病是人类最常见的非病毒性性传播感染。每年数以百万计的病例都有后遗症，包括怀孕期间的并发症和感染艾滋病毒的风险增加。阴道毛滴虫是滴虫病的病原体，滴虫病是世界上最普遍的非病毒性性传播感染。重复元件，包括转座元件（te）和病毒衍生的重复序列，占约160 mb阴道绦虫基因组的一半以上。一个有趣的问题是，寄生虫如何控制其潜在致命的可移动元素补充，这些元素可以破坏蛋白质编码基因的转录和基因组功能。在这项研究中，我们为阴道绦虫G3参考菌株建立了高通量RNA测序（RNA- seq）和小RNA- seq数据集，并对所有六条染色体上的mRNA和小RNA群体及其作图模式进行了表征。将RNA-Seq转录本映射到基因组显示，在重复元件中预测的大多数基因没有表达。有趣的是，我们发现了一种新的小RNA，它沿着染色体双向定位，与重复元件中蛋白质编码基因表达减少和RNA- seq覆盖减少相关。这个新的小RNA家族可能在基因和重复元件的表达中起调节作用。我们的研究结果确定了寄生虫调节基因和TEs表达的可能的小RNA途径机制，并提出了关于重复序列在塑造阴道绦虫基因组进化和小RNA途径多样性中的作用的有趣问题。滴虫病是由原虫阴道毛滴虫引起的，是人类最常见的非病毒性性传播感染。每年数以百万计的病例都有后遗症，包括怀孕期间的并发症和感染艾滋病毒的风险增加。鉴于它在这个生态位上的明显成功，阴道绦虫在其基因组中含有数千个对正常基因组功能极其有害的转座因子是矛盾的。在许多生物体中，转座子的表达是由内源性表达的短（~ 21 ~ 35个核苷酸[nt]）小RNA分子的活性调控的，这些小RNA分子通过靶向mrna降解或将表观遗传沉默机制招募到基因组中的位置来影响基因沉默。我们的研究已经确定了与阴道T.基因和转座子表达减少相关的小RNA分子。这表明小RNA通路是寄生虫基因表达模式的主要贡献者，为研究小RNA的生物发生、功能和多样性开辟了新的途径。
Trichomoniasis, caused by the protozoan Trichomonas vaginalis, is the most common nonviral sexually transmitted infection in humans. The millions of cases each year have sequelae that may include complications during pregnancy and increased risk of HIV infection. Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent nonviral sexually transmitted infection worldwide. Repetitive elements, including transposable elements (TEs) and virally derived repeats, comprise more than half of the ∼160-Mb T. vaginalis genome. An intriguing question is how the parasite controls its potentially lethal complement of mobile elements, which can disrupt transcription of protein-coding genes and genome functions. In this study, we generated high-throughput RNA sequencing (RNA-Seq) and small RNA-Seq data sets in triplicate for the T. vaginalis G3 reference strain and characterized the mRNA and small RNA populations and their mapping patterns along all six chromosomes. Mapping the RNA-Seq transcripts to the genome revealed that the majority of genes predicted within repetitive elements are not expressed. Interestingly, we identified a novel species of small RNA that maps bidirectionally along the chromosomes and is correlated with reduced protein-coding gene expression and reduced RNA-Seq coverage in repetitive elements. This novel small RNA family may play a regulatory role in gene and repetitive element expression. Our results identify a possible small RNA pathway mechanism by which the parasite regulates expression of genes and TEs and raise intriguing questions as to the role repeats may play in shaping T. vaginalis genome evolution and the diversity of small RNA pathways in general. IMPORTANCE Trichomoniasis, caused by the protozoan Trichomonas vaginalis, is the most common nonviral sexually transmitted infection in humans. The millions of cases each year have sequelae that may include complications during pregnancy and increased risk of HIV infection. Given its evident success in this niche, it is paradoxical that T. vaginalis harbors in its genome thousands of transposable elements that have the potential to be extremely detrimental to normal genomic function. In many organisms, transposon expression is regulated by the activity of endogenously expressed short (∼21 to 35 nucleotides [nt]) small RNA molecules that effect gene silencing by targeting mRNAs for degradation or by recruiting epigenetic silencing machinery to locations in the genome. Our research has identified small RNA molecules correlated with reduced expression of T. vaginalis genes and transposons. This suggests that a small RNA pathway is a major contributor to gene expression patterns in the parasite and opens up new avenues for investigation into small RNA biogenesis, function, and diversity.