Departamentode Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.
Laboratorio de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, 18016 Granada, Spain.
Int J Mol Sci. 2022 Aug 28;23(17):9761. doi: 10.3390/ijms23179761.
ticks are distributed across Europe and are a vector of tick-borne diseases. Although transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non-coding RNA (lncRNA) research and characterization. Here, we report for the first time an exhaustive analysis of these non-coding molecules in based on 131 RNA-seq datasets from three different BioProjects. Using this data, we obtained a consensus set of lncRNAs and showed that lncRNA expression is stable among different studies. While the length distribution of lncRNAs from the individual data sets is biased toward short length values, implying the existence of technical artefacts, the consensus lncRNAs show a more homogeneous distribution emphasizing the importance to incorporate data from different sources to generate a solid reference set of lncRNAs. KEGG enrichment analysis of host miRNAs putatively targeting lncRNAs upregulated upon feeding showed that these miRNAs are involved in several relevant functions for the tick-host interaction. The possibility that at least some tick lncRNAs act as host miRNA sponges was further explored by identifying lncRNAs with many target regions for a given host miRNA or sets of host miRNAs that consistently target lncRNAs together. Overall, our findings suggest that lncRNAs that may act as sponges have diverse biological roles related to the tick-host interaction in different tissues.
蜱虫分布于整个欧洲，是蜱传疾病的传播媒介。尽管转录组研究仅专注于蛋白质编码基因，但在过去十年中，长非编码 RNA（lncRNA）的研究和鉴定取得了长足的发展。在这里，我们首次根据来自三个不同 BioProjects 的 131 个 RNA-seq 数据集，对这些非编码分子进行了详尽的分析。利用这些数据，我们获得了一个 lncRNA 的共识集，并表明 lncRNA 的表达在不同研究中是稳定的。虽然来自各个数据集的 lncRNA 的长度分布偏向于短长度值，暗示存在技术伪影，但共识 lncRNA 显示出更均匀的分布，这强调了整合来自不同来源的数据对于生成可靠的 lncRNA 参考集的重要性。对宿主 miRNA 进行 KEGG 富集分析，这些 miRNA 可能靶向喂食后上调的 lncRNA，结果表明这些 miRNA 参与了与蜱虫-宿主相互作用相关的几个重要功能。通过鉴定具有给定宿主 miRNA 或一组宿主 miRNA 一致靶向 lncRNA 的许多靶区的 lncRNA，进一步探讨了至少一些蜱虫 lncRNA 可能作为宿主 miRNA 海绵的可能性。总体而言，我们的研究结果表明，可能作为海绵的 lncRNA 在不同组织中具有与蜱虫-宿主相互作用相关的多样化生物学功能。
