Figure 2

DNA methylation patterns in protein-coding genes and transposons in soybean cotyledons. (a) End analysis of ^mCG, ^mCHG, and ^mCHH levels for each bin in gene bodies and in 4 kb upstream of the transcription start site (TSS) and 4 kb downstream of the transcription termination site (TTS) in leaf and cotyledon at S2, S6, and S8. (b) End analysis of ^mCG, ^mCHG, and ^mCHH levels in leaf and cotyledon in the following transposons and their 4 kb upstream and downstream flanking regions: Helitron DNA transposons, Long Interspersed Nuclear Element (LINE) retrotransposons, Long Terminal Repeat (LTR) retrotransposons, and Terminal Inverted Repeat (TIR) DNA transposons. The upstream, gene body and downstream regions were divided into 100 bins respectively. Percentage of methylation in each bin is shown on Y-axis.