Main menu

Nanopore sequencing enables comprehensive transposable element epigenomic profiling


In cancers, but not healthy tissues, LINE-1 “jumping genes” insert throughout the genome, sometimes activating oncogenes and disrupting tumour suppressor genes. While CpG methylation regulates LINE-1 activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of LINE-1s in paired tumour and non-tumour liver as well as healthy tissues. We find pronounced demethylation of LINE-1s in cancer, allele-specific LINE-1 methylation, and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumour-specific LINE-1 insertions.

Authors: Seth Cheetham

Getting started

Buy a MinION starter pack Nanopore store Sequencing service providers Channel partners

Nanopore technology

Subscribe to Nanopore updates Resources and publications What is the Nanopore Community

About Oxford Nanopore

News Company timeline Sustainability Leadership team Media resources & contacts For investors For partners Working at Oxford Nanopore Current vacancies Commercial information BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
English flag