Genome-Wide Identification of CircRNAs of Infective Larvae and Adult Worms of Parasitic Nematode, Haemonchus contortus.
Genome-Wide Identification of CircRNAs of Infective Larvae and Adult Worms of Parasitic Nematode, Haemonchus contortus.
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寄生线虫捻转血矛线虫感染性幼虫和成虫 CircRNA 的全基因组鉴定
DOI：
10.3389/fcimb.2021.764089
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发表时间：
2021
影响因子：
5.7
通讯作者：
Hu M
中科院分区：
文献类型：
--
作者：
Zhou C;Zhang Y;Wu S;Wang Z;Tuersong W;Wang C;Liu F;Hu M
CircRNAs是一类新发现的ncRNA家族，是参与动植物多种生物生理过程的内源性转录产物。然而，几乎没有关于寄生蠕虫的CircRNA的信息。本研究对反刍动物的一种吸血寄生线虫缠绕血线虫的CircRNAs谱进行了全面的研究。通过深度测序技术和生物信息学分析，共鉴定和注释了旋毛虫三个关键发育阶段/性别的20073个CircRNA，包括自由生活的感染性第三期幼虫(L3,18883)、寄生成虫(Af，3491)和雄虫(Am，2550)。在这些已鉴定的CircRNA中，71%来自蛋白质编码基因的外显子区域。X染色体转录的CircRNA数(4704)高于I-V染色体(3143、3273、3041、3030、2882)。第三期幼虫高表达的CircRNAs数量明显多于成虫期。Af和L3s之间、Am和L3之间分别有15948和16847个CircRNA差异表达。其中，在两次比较中均存在13409个CircRNA。此外，有1119个CircRNA在Af_和_Am之间有差异表达。GO富集分析表明，在Am和L3以及Af和L3之间差异表达的CircRNAs的源基因在许多生物学过程中都显著富含，主要包括信号转导和细胞通讯条件。KEGG分析表明，差异表达的CircRNAs的亲本基因主要与代谢(丙酮酸代谢、甘油磷脂代谢和碳代谢)、MAPK信号通路和磷脂酰肌醇信号系统有关。此外，许多CircRNAs含有一个或多个miRNA潜在结合位点，这表明它们可以在转录后水平上调节基因表达。此外，使用发散和收敛两种引物进行Sanger测序，验证了头尾向后剪接位点和交替环化事件的正确性。最后，通过定量RT-PCR验证了RNA-Seq数据的可靠性和CircRNAs对RNase R消化的抗性。综上所述，我们的发现为阐明缠绕线虫CircRNAs的调控机制提供了基础，这将促进对寄生线虫CircRNAs的理解。
CircRNAs, a novel class of ncRNA family, are endogenous transcriptional products involved in various biological and physiological processes in plants and animals. However, almost no information is available for circRNAs of parasitic helminths. In the present study, the circRNAs repertoire was comprehensively explored in Haemonchus contortus, a blood-sucking parasitic nematode of ruminants. In total, 20073 circRNAs were identified and annotated from three key developmental stages/genders of H. contortus including the free-living infective third-stage larvae (L3, 18883), parasitic adult female (Af, 3491), and male worms (Am, 2550) via deep-sequencing technology and bioinformatic analysis. Among these identified circRNAs, 71% were derived from exonic regions of protein-coding genes. The number of circRNAs transcribed from the X chromosome (4704) was higher than that from Chromosome I-V (3143, 3273, 3041, 3030, 2882). The amount of highly expressed circRNAs in third-stage larvae was significantly more abundant than that in adult stage. 15948 and 16847 circRNAs were differentially expressed between Af and L3s and between Am and L3, respectively. Among them, 13409 circRNAs existed in both comparisons. Furthermore, 1119 circRNAs were differentially expressed between Af_and_Am. GO enrichment analysis indicated that source genes of circRNAs differentially expressed between Am and L3 as well as between Af and L3 were significantly enriched in many biological processes, primarily including signaling, signal transduction and cell communication terms. KEGG analysis revealed that parental genes of differentially expressed circRNAs were mainly related to metabolism (pyruvate metabolism, glycerophospholipid metabolism, and carbon metabolism), MAPK signaling pathway, and phosphatidylinositol signaling system. Moreover, many circRNAs contained one or more miRNA potential binding sites, suggesting that they could regulate gene expression at the post-transcriptional level. Furthermore, the correctness of head-to-tail back splicing site and alternative circularization events were verified by Sanger sequencing using both divergent and convergent primers. Finally, the reliability of RNA-Seq data and the resistance of circRNAs to RNase R digestion were confirmed by quantitative RT-PCR. Taken together, our findings provide a foundation for elucidating the regulatory mechanisms of circRNAs in H. contortus, which will advance the understanding of circRNAs in parasitic nematodes.
探索捻转血矛线虫两种相互作用的磷酸肌醇 3-激酶的作用
影响因子：
3.2
作者：
Li FC;Gasser RB;Lok JB;Korhonen PK;Wang YF;Yin FY;He L;Zhou R;Zhao JL;Hu M
通讯作者：
Hu M