Xu Jiannong, Hu Kai, Riehle Michelle M, Khadka Vedbar S
Department of Biology, New Mexico State University. Las Cruces NM, USA.
Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School. Worcester, Massachusetts, USA.
Front RNA Res. 2025;3. doi: 10.3389/frnar.2025.1555885. Epub 2025 Apr 15.
is a primary malaria vector mosquito in Africa. RNA-seq based transcriptome analysis has been widely used to study gene expressions underlying mosquito life traits such as development, reproduction, immunity, metabolism, and behavior. While it is widely appreciated that long non-coding RNAs (lncRNAs) are expressed ubiquitously in transcriptomes across metazoans, lncRNAs remain relatively underexplored in , including their identity, expression profiles, and biological functions. The lncRNA genes were poorly annotated in the current reference of the PEST genome of . In this study, a set of publicly available RNA-seq datasets was leveraged to identify lncRNAs across diverse contexts, including whole mosquitoes, mosquito cells or tissues including hemocytes, midguts, and salivary glands, as well as under different physiological conditions including sugar-feeding, blood-feeding, bacterial challenges, and infections. A Transcript Discovery module implemented in CLC genomics workbench was used to identify lncRNAs from selected published RNA-seq datasets. Across this pool of transcriptomes, 2684 unique lncRNA genes, comprising 4082 transcripts, were identified. Following their identification, these lncRNA genes were integrated into the mosquito transcriptome annotation, which was then used as a reference to analyze both mRNAs and lncRNAs for transcriptional dynamics in different conditions. Unsurprisingly and similar to what has been reported for mRNAs, lncRNAs exhibited context-dependent expression patterns. Co-expression networks constructed using weighted gene co-expression network analysis (WGCNA) highlighted the interconnections among lncRNAs and mRNAs, which provides potential functional networks in which these lncRNAs are involved. Furthermore, we identified polysome-associated lncRNAs within polysome-captured transcripts, suggesting the involvement of lncRNAs in translation regulation and coding capacity for micropeptides. The analysis of a ChIP-seq dataset unveiled a correlation of transcriptional activities between lncRNAs and observed epigenetic signatures. Overall, our study demonstrated that lncRNAs are transcribed alongside mRNAs in various biological contexts. The genome-wide annotation of lncRNA genes and integration into the PEST reference genome enables the co-analysis of mRNA and lncRNA simultaneously, which will enhance our understanding of their functions, shedding light on their regulatory roles in biology.
是非洲主要的疟疾传播媒介蚊子。基于RNA测序的转录组分析已被广泛用于研究蚊子生命特征（如发育、繁殖、免疫、代谢和行为）背后的基因表达。虽然人们普遍认识到长链非编码RNA（lncRNA）在整个后生动物的转录组中普遍表达，但在（此处缺少具体物种名称）中，lncRNA的研究仍相对较少，包括它们的身份、表达谱和生物学功能。在（此处缺少具体物种名称）的PEST基因组的当前参考中，lncRNA基因注释不佳。在本研究中，利用一组公开可用的RNA测序数据集来识别不同情况下的lncRNA，包括整个蚊子、蚊子细胞或组织（包括血细胞、中肠和唾液腺），以及在不同生理条件下（包括取食糖水、取食血液、细菌攻击和（此处缺少具体感染类型）感染）。使用CLC基因组学工作台中实现的转录本发现模块从选定的已发表RNA测序数据集中识别lncRNA。在这组转录组中，共鉴定出2684个独特的lncRNA基因，包括4082个转录本。在鉴定出这些lncRNA基因后，将它们整合到蚊子转录组注释中，然后将其用作参考，以分析不同条件下mRNA和lncRNA的转录动态。不出所料，与mRNA的报道相似，lncRNA表现出依赖于上下文的表达模式。使用加权基因共表达网络分析（WGCNA）构建的共表达网络突出了lncRNA和mRNA之间的相互联系，这提供了这些lncRNA所涉及的潜在功能网络。此外，我们在多核糖体捕获的转录本中鉴定出与多核糖体相关的lncRNA，表明lncRNA参与翻译调控以及微肽的编码能力。对ChIP-seq数据集的分析揭示了lncRNA的转录活性与观察到的表观遗传特征之间的相关性。总体而言，我们的研究表明，lncRNA在各种生物学背景下与mRNA一起转录。lncRNA基因的全基因组注释以及整合到PEST参考基因组中能够同时对mRNA和lncRNA进行共分析，这将增进我们对它们功能的理解，揭示它们在（此处缺少具体物种名称）生物学中的调控作用。
