Main menu

Nanopore sequencing enables comprehensive transposable element epigenomic profiling


Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE 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 novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver.

As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues.

Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.

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

入門

MinION Starter Packを購入 ナノポア製品の販売 シークエンスサービスプロバイダー グローバルディストリビューター

お問い合わせ

Intellectual property Cookie policy Corporate reporting Privacy policy Terms & conditions Accessibility

Oxford Nanoporeについて

Contact us 経営陣 メディアリソース & お問い合わせ先 投資家向け Oxford Nanopore社で働く BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Japanese flag