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

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.

A new role for histone demethylases in the maintenance of plant genome integrity

“…We analysed Bisulfite-seq data using Bismark ( Krueger and Andrews, 2011 ) using the following parameters:–bowtie2 –ambiguous –unmapped –R 10 –score_min L,0,–0.6 -N 1. Identification of new TE insertion sites was performed using epiTEome ( Daron and Slotkin, 2017 ). For the validation of new transposon insertions, we designed primers outside of predicted TE insertion site and inside the transposon based on physical reads identified by epiTEome.…”

Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

“…Of the 50,339 TEs that lost over 50% CG methylation, only 284 (0.6%) were differentially expressed in 8 year globular embryos relative to the initial stage. To assess if any of the loss in methylation leads to novel TE insertions, we used epiTEome (Daron and Slotkin, 2017) and identified a subtle increase in TE insertion events over time (Supplemental Figure 8). However, different integration events were found at all stages compared with the 24 h-2,4-D stage, suggesting that the TEs present in this genotype do not accumulate during tissue culture.…”

“…Identification of nonreference TE insertions was performed using epi-TEome as described (Daron and Slotkin, 2017). Only TEs that were not present in the 24 h-2,4-D were outputted.…”

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

“…However, this method is focused on a very particular type of human TEs but it probably may be possible to consider its adaptation to other types of TEs. Recently, a new bioinformatic method, EpiTEome, has been proposed with the simultaneous goal to detect both TE insertion sites and their DNA methylation level [127]. This approach allows detecting, in addition to known TE insertions, any new insertions.…”