Fig. 1

Histone markers enrichment across different platforms and loci. A Venn diagrams showing comparison between Illumina and microarray data for H4ac-associated genes. Comparison of H4ac-associated loci identified in three conditions of interest on different platforms: Illumina HiSeq replicates of ChIP-Seq data, and comparison of this data on the transcriptome level with microarray analysis. For Illumina, genes were considered to be significant in that condition if the peak summit generated by MACS was situated within identified loci. In the microarray data, genes with at least a 2-fold difference in their expression levels were evaluated with Student’s t test, and genes with p-values < 0.05 were counted as differentially expressed in the condition of interest. Diagrams created in BioVenn [73]. B Up- and downregulated genes identified by microarray analysis in three conditions of interest compared to the untreated WT control. C Histone marker enrichment distribution 2.0 kb upstream of transcription start sites (TSSs) and downstream of transcription termination sites (TTSs). The log2 ratio of ChIP signal to input on aligned files was calculated for both H4ac (upper panel) and H3K27me3 (lower panel) histone modifications using bamCompare from the deepTools2 package (Galaxy version 3.0.2.0) [74, 75] on WT and axe1-5-untreated and MeJA-treated samples. One representative replicate is shown