Nanopore sequencing enables comprehensive transposable element epigenomic profiling

Adam D. Ewing; Nathan Smits; Francisco Jose Sanchez-Luque; Jamila Faivre; Paul Martin Brennan; Sandra R. Richardson; Seth W. Cheetham; Geoffrey J. Faulkner

doi:10.1016/j.molcel.2020.10.024

GenomicsMolecular CellNov 12, 2020

Peer-reviewed journal article

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

Adam D. Ewing iD, Nathan Smits iD, Francisco Jose Sanchez-Luque iD, Jamila Faivre iD, Paul Martin Brennan iD, Sandra R. Richardson iD, Seth W. Cheetham iD, Geoffrey J. Faulkner iD

Abstract

We apply long-read nanopore sequencing and a new tool, TLDR (Transposons from Long Dirty Reads), to directly infer CpG methylation of new and extant human transposable element (TE) insertions in hippocampus, heart, and liver, as well as paired tumour and non-tumour liver. Whole genome TLDR analysis greatly facilitates studies of TE biology as complete insertion sequences and their epigenetic modifications are readily obtainable.

PDF DOI