Differences in directionality of RNA polymerase initiation underlie epigenome differences between plants and animals
Transcriptional regulation is a universal mechanism for a wide array of biological processes, and is driven in large part by genetic enhancer elements. These regulatory elements have been well-studied in animal species, yet their plant counterparts remain poorly characterized.  While high-throughput profiling of animal genomes has yielded great success in identifying genetic enhancers through secondary characteristics – flanking histone posttranslational modifications (PTMs), chromatin accessibility, and the production of enhancer RNAs (eRNAs) – it is an active line of investigation as to whether these secondary characteristics can be used in a similar way to locate regulatory regions of plant genomes.  Here, we compare the enrichment of the four histone PTMs most commonly associated with animal enhancers – H3K27ac, H3K27me3, H3K4me1, and H3K4me3 – between Drosophila melanogaster, Homo sapiens, and Arabidopsis thaliana genomes. Regions of accessible chromatin were identified through ATAC-seq or DNase-seq, and were analyzed as putative enhancer regions.  Additionally, as it has been shown that enhancer activity varies widely from cell type to cell type, matched, single-cell type datasets were used for each species whenever available.  Through the intersection of these data it becomes clear that there are distinct differences between the epigenetic makeup of plant and animal genomes.  While these four histone PTMs are present at transcription start sites (TSSs) in all three of the species investigated, A. thaliana showed a marked depletion of these modifications upstream of the TSS, while the animal species showed bimodal enrichment.  The plant histone PTM pattern is consistent with the pattern observed at unidirectional promoters, which was further supported by GRO-seq data.  When intergenic regions of accessible chromatin were examined – putative enhancer regions – the plant epigenomes showed a one-sided, rather than bimodal, enrichment of all four of the histone PTMs.  However, these sites retain the ability to produce eRNAs, suggesting that they are likely functionally active enhancer elements.  While it is known that animal promoters and enhancers have bidirectional transcription, this analysis revealed that plant promoters and enhancers have a distinct pattern, and only exhibit histone PTM deposition and transcription in the sense direction.  While further investigation is merited, this may speak to a fundamental difference between the transcriptional machinery of plant and animal kingdoms. Overall design: Examination of enhancer histone modification enrichment across the Arabidopsis epigenome using single cell-type data