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Related Experiment Video

Updated: Nov 30, 2025

Reusable Single Cell for Iterative Epigenomic Analyses

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Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling.

Adam D Ewing¹, Nathan Smits¹, Francisco J Sanchez-Luque²

¹Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.

|November 13, 2020

Summary

This summary is machine-generated.

Cancer demethylates young LINE-1 retrotransposons, unlike other TEs or normal tissue, revealing insights into genome evolution and pathogenesis. Long-read sequencing maps these epigenetic changes and tumor-specific insertions.

Keywords:

Alu LINE-1 SVA methylation nanopore retrotransposon

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Area of Science:

Genomics
Epigenetics
Molecular Biology

Background:

Transposable elements (TEs) significantly influence genome evolution and are implicated in diseases like cancer.
CpG methylation is a key regulator of TE activity, but its locus-specific patterns in human mobile TEs remain largely uncharacterized.

Purpose of the Study:

To directly infer the CpG methylation landscape of novel and existing transposable element insertions across various human tissues and in paired tumor/non-tumor samples.
To investigate the relationship between TE methylation, TE activity, and cancer development.

Main Methods:

Application of advanced computational tools combined with long-read nanopore sequencing.
Direct inference of CpG methylation for transposable elements in hippocampus, heart, liver, and matched tumor/non-tumor liver tissues.

Main Results:

Young long interspersed element 1 (LINE-1) retrotransposons exhibit significant demethylation in cancer, distinct from adjacent genomic regions and other TEs.
SINE-VNTR-Alu (SVA) retrotransposons, including their associated CpG islands, are consistently methylated.
Allele-specific methylation and demethylation patterns were observed in aberrantly expressed young LINE-1s within normal tissues.
Complete sequences of tumor-specific LINE-1 insertions and their retrotransposition markers were identified.

Conclusions:

Cancer-associated demethylation of young LINE-1s is a specific epigenetic event, not a stochastic process.
Long-read sequencing offers a powerful, simultaneous approach to epigenome surveying and somatic transposable element mobilization detection.
Findings provide novel insights into the role of epigenetics in TE regulation and cancer pathogenesis.