Over the past 20 years, high-throughput genomic assays have fundamentally changed how transposable elements (TEs) are studied. While short-read DNA sequencing has been at the heart of these efforts, novel technologies that generate longer reads are driving a shift in the field. Long-read sequencing now permits locus-specific approaches to locate individual TE insertions and understand their epigenetic and transcriptional regulation, while still profiling TE activity genome-wide. Here we provide detailed guidelines to implement Oxford Nanopore Technologies (ONT) sequencing to identify polymorphic TE insertions and profile TE epigenetic landscapes. Using human long interspersed element-1 (LINE-1, L1) as an example, we explain the procedures involved, including final visualization, and potential bottlenecks and pitfalls. ONT sequencing will be, in our view, a workhorse technology for the foreseeable future in the TE field.
CITATION STYLE
Smits, N., & Faulkner, G. J. (2023). Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications. In Methods in Molecular Biology (Vol. 2607, pp. 151–171). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2883-6_9
Mendeley helps you to discover research relevant for your work.