ABSTRACT

Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.

摘要

长链非编码 RNA (lncRNA) 是一组异质的转录本，它们缺乏蛋白质编码潜力并在各种细胞过程中表现出调节功能。由于它们的细胞和癌症特异性表达模式，lncRNA 已成为潜在的诊断和治疗靶点。由于与蛋白质编码基因相比，lncRNA 的丰度较低，因此在批量转录组数据中准确表征 lncRNA 仍然具有挑战性。为了解决这个问题，我们描述了一种独特的短读长定制 lncRNA 捕获测序方法，该方法依赖于针对 49,372 个人类 lncRNA 基因的 565,878 个捕获探针的综合集合。这种定制的 lncRNA 捕获方法在从人工高质量 RNA 混合物到更具挑战性的福尔马林固定石蜡包埋组织和生物流体材料的各种样本类型上进行了评估。