Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5′ gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type–specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.

中文翻译：

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通过小鼠海马单核 RNA-seq 鉴定真正的 B2 SINE 反转录转座子转录

目前，研究人员依靠通用方法来量化转座因子 (TE) RNA 表达，例如 RT-qPCR 和 RNA-seq，这些方法不区分从它们自己的启动子（真正的）表达的 TE 和从相邻启动子转录的 TE基因启动子，例如在内含子或外显子中。这种区别很重要，因为 TE 的功能作用不同，具体取决于它们是否独立转录。在这里，我们报告了一种检查真实 TE 表达的简单策略，称为 BonaFide-TEseq。这种方法可用于任何基于模板转换的库，例如 Smart-seq2 或 10x 的单细胞 5' 基因表达试剂盒，将其效用扩展到单细胞 RNA 测序。这种方法不需要 TE 特异性富集，可以同时检查 TE 和蛋白质编码基因。我们表明，通过 BonaFide-TEseq 鉴定的 TE 是从它们自己的启动子表达的，而不是作为基因的内部产物捕获的。我们揭示了 BonaFide-TEseq 在单细胞数据分析中的效用，并表明短散布核元件 (SINE) 在小鼠海马体中显示了细胞类型特异性表达谱。我们进一步表明，作为对笼养小鼠短暂暴露于新刺激的响应，SINE 在齿状颗粒神经元中被激活的时间过程类似于蛋白质编码的直接早期基因。这项工作提供了一种简单的替代方法来评估单细胞分辨率下的真实 TE 转录，并提供了使用此方法在与正常学习和记忆相关的上下文中识别 SINE 激活的概念验证。