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Fig. 5 | Genome Biology

Fig. 5

From: Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

Fig. 5

Non-TE-DEGs in met1 mutants can have different epigenetic states in different accessions. a Heatmap of expression changes across 5731 Non-TE-DEGs in 17 accessions, with an adjacent heatmap showing variance expressed as standard deviation (SD) across accessions, and scatterplots of changes in expression and accessibility in representative genes, AT1G60190 and PR1, from two different DEG categories (based on overlap with cis CG-DMRs and HV-dACRs). A genome browser screenshot of ATAC-seq, RNA-seq, and BS-seq data in three accessions is shown for a third example gene locus, ROS1, harboring both cis DMRs and cis dACRs. b Scatterplot of changes in chromatin accessibility and methylation in Non-TE-DEGs across 17 accessions. Colors and density distributions represent custom bins of expression changes. A closeup of a selected region is shown below. c Scatterplots similar to b for Non-TE genes. d Boxplots showing MET1-dependent changes in chromatin accessibility, gene expression, and CG methylation of genes that are weakly (“LOW”) or highly (“HIGH”) methylated in wild-type Cvi-0. The same genes are compared for Cvi-0 (dark green) and 16 other accessions (gray). e Scatterplot of changes in methylation and expression in Non-TE-DEGs with gene body CG-DMRs, colored by DEGs specific to Col-0 (black) against the same genes in other accessions (yellow). f Scatterplot of changes in chromatin accessibility and expression in Non-TE-DEGs carrying cis dACRs, colored by DEGs specific to Col-0 (black) against the same genes in other accessions (yellow). Expression levels are represented as transformed read counts (tr. counts); chromatin accessibility levels as TMM (trimmed mean of M-values) normalized values in counts per million (CPM), and methylation levels as % CG methylation

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