Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900, Sao Paulo, SP, Brazil.
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900, Sao Paulo, SP, Brazil.
Sci Rep. 2017 Sep 5;7(1):10508. doi: 10.1038/s41598-017-10853-6.
Next Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomiasis, ranked among the most prevalent parasitic diseases worldwide. We focused on the long intergenic/intervening ncRNAs (lincRNAs), hidden within the large amount of information obtained through RNA-Seq in S. mansoni (88 libraries). Our computational pipeline identified 7029 canonically-spliced putative lincRNA genes on 2596 genomic loci (at an average 2.7 isoforms per lincRNA locus), as well as 402 spliced lncRNAs that are antisense to protein-coding (PC) genes. Hundreds of lincRNAs showed traits for being functional, such as the presence of epigenetic marks at their transcription start sites, evolutionary conservation among other schistosome species and differential expression across five different life-cycle stages of the parasite. Real-time qPCR has confirmed the differential life-cycle stage expression of a set of selected lincRNAs. We have built PC gene and lincRNA co-expression networks, unraveling key biological processes where lincRNAs might be involved during parasite development. This is the first report of a large-scale identification and structural annotation of lncRNAs in the S. mansoni genome.
下一代测序（NGS）策略，如 RNA-Seq，已经揭示了几种生物基因组中转录了大量长非编码 RNA（lncRNA）。在本工作中，我们评估了曼氏血吸虫的 lncRNA 组成，曼氏血吸虫是引起血吸虫病的血吸，属于全球最普遍的寄生虫病之一。我们专注于长基因间/间插 ncRNA（lincRNA），这些 lincRNA 隐藏在 RNA-Seq 在 S. mansoni 中获得的大量信息中（88 个文库）。我们的计算管道在 2596 个基因组座上识别了 7029 个规范剪接的推定 lincRNA 基因（每个 lincRNA 基因座平均有 2.7 个异构体），以及 402 个与蛋白编码（PC）基因反义的剪接 lncRNA。数百个 lincRNA 表现出具有功能的特征，例如在转录起始位点存在表观遗传标记、在其他血吸虫物种中进化保守以及在寄生虫的五个不同生命周期阶段的差异表达。实时 qPCR 已经证实了一组选定的 lincRNA 在不同生命周期阶段的差异表达。我们构建了 PC 基因和 lincRNA 共表达网络，揭示了 lincRNA 在寄生虫发育过程中可能参与的关键生物学过程。这是首次在 S. mansoni 基因组中大规模鉴定和结构注释 lncRNA。
