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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

Design of epiTEome function. a Workflow of methodology developed to identify non-reference insertions of TEs using filtered MethylC-seq reads that fail to align to the reference genome. b Principle behind split-read detection of new TE insertion sites. Reads that fail to fully map to the reference genome are used to identify the sites of new TE insertion. Non-mapping reads are split and mapped to the reference genome to identify reads with one end that maps to a TE and the other end to the site of insertion. c Example of a new TE insertion detected by epiTEome in Arabidopsis: ddm1 mutants undergo TE transcriptional reactivation and transposition [30]. Split reads not present in wild-type (wt Col-0) identify a TE insertion into the gene At2g34840 in two biological replicates of ddm1 MethylC-seq (RepA and RepB). The 5′ and 3′ flanking spit reads overlap (dashed lines) at the target site duplication (gold sequence) generated by TE insertion. d In addition to identifying new TE insertion sites, epiTEome detects the cytosine methylation status at these loci. Sequence alignment of split MethylC-seq reads at the insertion site are used to determine the cytosine DNA methylation status. Unconverted cytosines represent methylated bases, while C → T transitions (bold) in the MethylC-seq reads represent unmethylated cytosines. The sequence context of each cytosine is displayed (CG = red, CHG = blue, CHH = green)

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