Fig. 5

Dynamic changes in chromatin marks in nitrate replete and limiting conditions. a Venn diagrams showing overlap of different histone marks on genes in nitrate replete (Normal N) and nitrate-limiting (Low N) conditions. b Venn diagrams showing overlap of different histone marks on TEs in nitrate replete and nitrate-limiting conditions. Percentages of differentially marked genes and TEs are indicated between parentheses. c Comparison of levels of ChIP binding and expression levels. Fold change of ChIP binding (differential binding) is calculated from the number of reads in the peak region using diffReps. Fold change in expression level is calculated from the levels of RPKM using the Cuffdiff [78]. Pearson correlation values between differentially marked and expressed genes under the two conditions (normal and low nitrate growth conditions) are marked along the trend line. d Number of genome features (genes and transposable elements) marked by each of the three histone marks, as well as DNA methylation. Percentage was derived using the known genome feature annotations. Number of genes, TEs and intergenic regions under normal or low nitrate are indicated above each bar