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

ABSTRACT: 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 express

SUBMITTER: Li X 

PROVIDER: S-EPMC10517987 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature