Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Micrographia Bio, London, W12 0BZ, UK.
BMC Genomics. 2022 Nov 30;23(1):780. doi: 10.1186/s12864-022-09017-2.
Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum.
We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes.
The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.
疟原虫（Plasmodium falciparum）在转录水平上发生重要调控，越来越多的证据表明这些顶复门寄生虫具有复杂的调控网络。最近的研究表明，长非编码 RNA（lncRNA）是疟原虫转录调控因子。然而，由于研究有限且缺乏必要的实验工具，我们对其在引起疟疾的寄生虫中的作用的理解在很大程度上仍未阐明。在这项工作中，我们解决了其中的一个限制因素，即疟原虫缺乏最新和改进的 lncRNA 注释。
我们生成了长读 RNA 测序数据，并整合了从多个来源提取和整理的信息，以手动注释 lncRNA。我们鉴定了 1119 个新的 lncRNA，并验证和细化了 1250 个现有的注释。利用整理好的数据集，我们为每个注释生成了基于证据的评分，并描述了疟原虫 lncRNA 的独特基因组上下文和特征。某些特征表明存在具有潜在生物学意义的子集，例如 25 个包含多个内含子的 lncRNA、335 个在 piggyBac 诱变研究中没有突变的 lncRNA，以及与特定生物学过程相关的 lncRNA，包括在 var 基因附近发现的两种新型 lncRNA。
本研究提供的见解和注释将为研究人员提供有价值的工具，通过生物信息学和实验方法来研究 lncRNA 在寄生虫生物学中的作用。
