EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels

Genome Biology
Josquin Daron, R Keith Slotkin

Abstract

The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads. EpiTEome characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements.

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Citations

May 11, 2018·Mobile DNA·R Keith Slotkin
Feb 23, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kathryn O'NeillMolly Gale Hammell
Sep 21, 2018·Nature Reviews. Genetics·Patricia Goerner-Potvin, Guillaume Bourque
Oct 28, 2020·ELife·Javier Antunez-SanchezJose Gutierrez-Marcos

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Methods Mentioned

BETA
MethylC-seq

Software Mentioned

Sherman
cutadapt
SPLITREADER
BioPerl
READSPLITER
Segemehl
bedtools Perl script
EpiTEome
TEPID
bedmap

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