capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

• Published in: Communications biology Vol. 6; no. 1; pp. 974 - 14
• Main Authors: Li, Xuemei, Lu, Keying, Chen, Xiao, Tu, Kailing, Xie, Dan
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.09.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 38/39; 38/43; 38/91; 631/1647/514/1949; 631/208/514/2256; 631/337/2019; Alu elements; Biology; Biomedical and Life Sciences; DNA Transposable Elements - genetics; Gene expression; Gene loci; Humans; Life Sciences; Mutagenesis, Insertional; Mutagens; Regulatory sequences; Regulatory Sequences, Nucleic Acid; Sequence Analysis, RNA; Transcription; Transcriptomes; Transposons
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-05349-1

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. capTEs is a long-read targeted RNA-sequencing method that can quantify the expression of reference and non-reference transposable elements at the level of genomic loci.