Fig. 3: Epigenetic regulation of ATE-G isoforms. | Nature Communications

Fig. 3: Epigenetic regulation of ATE-G isoforms.

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

Fig. 3

a Top: Number of genes in each mutant showing isoform switching of ATE-G isoforms detected in DRS-AtRTD3. Bottom: Number of genes in each mutant showing change in isoform usage of ATE-G isoforms detected in mutant-DRS dataset. b Representative genome loci showing epigenetically regulated ATE-G isoform (Epi-ATE-G isoform) production with TE-ATSS events. Tracks (from top to bottom): CAGE-seq (reads per million. Only forward or reverse strands are shown); Col-0 ChIP-seq of H3K9me2 (bin per million); methylation level of each mutant in CG, CHG, and CHH contexts (0–100%); DRS read alignments of Col-0 and indicated mutants; TE and AtRTD3 transcript annotations, de novo assembly of transcripts in mutants, and the orientation of genes and TEs. Red arrows on the top indicate cryptic TSSs detected in epigenetic mutants. c Epi-ATE-G isoform production and isoform switching detected at the AT2G40960 locus in ddm1. Top: ddm1-DRS transcripts aligned to the AT2G40960 locus. Middle: Isoform usage (IF) of ATE-G isoforms. Benjamini–Hochberg false discovery (FDR) corrected p-values (q-values; *, q < 0.05) for isoform switching. Bottom: Expression levels of isoforms. Error-bars indicate 95% confidence intervals. Adjusted p-value from DESeq2 (*, padj < 0.05).

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