转座元件（Transposable elements，TEs）在细胞中既能充当插入性诱变剂，又能作为调控元件，并且越来越多的研究结果表明它们的异常活性参与了疾病和癌症的发生。然而，目前的方法对非参考基因组和年轻的转座元件的转录后果进行定量分析仍然面临挑战，主要是因为技术上存在的限制，包括生成的短读长和目标区域的覆盖不足。在这里，我们引入了一种长读长的靶向RNA测序方法，称为Cas9辅助的转座元件表达测序（capTEs），用于定量分析单个转座元件的转录产物，包括转录的非参考插入物，来自不同转录模式的非规范转录本以及它们与相关基因表达变化的相关性。该方法能够选择性地识别出含有转座元件的转录本，并输出包含高达90%转座元件序列的数据，与整个转录组测序相比，数据产量基本相当。我们将capTEs应用于人类癌细胞，并发现内部和插入的Alu重复元件可能使用不同的调控机制上调基因表达。我们预计，capTEs将成为在基因座水平上推进我们对单个转座元件生物学功能理解的关键工具，揭示它们作为诱变剂和调控因子在生物学和致病过程中的作用。© 2023. Springer Nature Limited.

Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression. We expect that capTEs will be a critical tool for advancing our understanding of the biological functions of individual TEs at the locus level, revealing their roles as both mutagens and regulators in biological and pathogenic processes.© 2023. Springer Nature Limited.