Relationship between histone methylation and mRNA levels during and after priming. (A, B) Genes on the x-axis were ranked according to mRNA levels determined by RNA-Seq. The mRNA profiles shown as smooth lines were generated from plotting for each gene on the x-axis the average mRNA values (right y-axis) over the neighboring genes with ranks of +/-100. Average values of histone modification levels (A: H3K4me3, B: H3K27me3) were plotted for the same genes (left y-axis). Relationships for non-primed root samples (CR) are shown in the graphs on the left, those for primed root samples (PR) are shown in the graphs on the right. (C) Numbers of genes that show an increase (up) or decrease (down) of mRNA level (x-axis) or histone modification level (y-axis) in response to the priming treatment (primed compared to non-primed roots). Note that the majority of changes observed immediately after the priming treatment do not show the expected positive (H3K4me3) or negative (H3K27me3) correlation between mRNA and histone modification (dashed lines). (D) Short-term kinetics of changes of mRNA and H3K27me3 levels in three genes (HKT1, TEL1, and MYB75) during the priming treatment. Relative enrichment of H3K27me3 (black bars) and mRNA levels (open bars) of selected genes in roots of A. thaliana seedlings were determined by qPCR over a time course of the first 8 h (x-axis) of the priming treatment (50 mM NaCl). H3K27me3 enrichment (left y-axis) was normalized to ChIP input and to a reference region in At5g56920. mRNA levels (right y-axis) were normalized to reference gene RpII. Bars show means ± SE of four pairwise ratios of two technical replicates of qPCR carried out with pooled root material from approximately 50 plants per time point. Significant differences to time point 0 are indicated with * for P <0.01.
Sani et al. Genome Biology 2013 14:R59 doi:10.1186/gb-2013-14-6-r59