Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Abstract

Post-translational modifications of histones are important components of chromatin-level control of genome activity in eukaryotes. In order to clarify the biological function of chromatin marks, classification methods have been developed that partition genomic regions based on their chromatin composition. Spatial enrichment of histone modifications over genes is one of the many epigenomic dimensions that reflect the impact of chromatin dynamics on gene regulation. Using a clustering approach, we have classified genes according to their H3K27me3 and H3K4me3 marking in Arabidopsis leaves and find that multiple spatial profiles with specific functional properties can be distinguished in both cases. In particular, we show that different profiles specify distinct levels of gene expression. In addition, we find that genes with different H3K27me3 profiles can be distinguished by the length of their first intron and that the length of the first exon is an important parameter that shapes the distinct H3K4me3 profiles. Finally, we suggest that profile height could be quantitatively used to estimate the relative abundance of cells in which a gene is marked, and potentially expressed, within a tissue. © 2013 © 2013 Taylor & Francis.