Fig. 4: Epigenetic regulation of TE-ATTS. | Nature Communications

Fig. 4: Epigenetic regulation of TE-ATTS.

From: Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Fig. 4

a Representative genome loci showing Epi-ATE-G isoform production with TE-ATTS events. Tracks (from top to bottom): ChIP-seq data for RNA Pol II phosphorylated at Ser5/Ser2 in CTD repeats (bins per million); ChIP-seq data for IBM2 and EDM2 localization (bins per million); Col-0 ChIP-seq of H3K9me2 (reads per million); methylation levels of Col-0 in CG, CHG, and CHH contexts (0–100%); poly(A) sites obtained from the PlantAPA database; DRS read alignments of Col-0 and indicated mutants; TE and transcript annotations of AtRTD3 and DRS-AtRTD3 in this study and the orientation of genes and TEs. b Metaplots for ChIP-seq signals of Pol II (Ser2P), IBM2, EDM2, and H3K9me2 over TEs with ATTS (isoform switching with q < 0.05 detected at least once among mutants; Supplementary Data 5; n = 223) or randomly selected TEs (n = 223). c Changes in Pol II (Ser2P) ChIP-seq signals in TEs with ATTS (n = 223) between the wild-type and mutants. The centerline represents the median. The borders of the boxplots are the first and third quartiles (Q1 and Q3). Whiskers represent data range, bounded to 1.5 * (Q3-Q1). Source data are provided as a Source Data file.

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