Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27


Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are more substantial differences in the genome-wide profile of H3K27me3 between different tissues than between the two genotypes. The tissue-specific patterns of H3K27me3 are often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. Many maize genes with important developmental roles, including numerous genes encoding putative transcription factors, are modified with H3K27me3 in at least one of the tissues that were profiled. A comparison of the H3K27me3 targets in rice, maize, and Arabidopsis provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole genome duplication, suggesting the potential for sub-functionalization of chromatin regulation of paralogs. Genomic profiling of H3K27me3 in loss-of-function mutant stocks for Mez2 and Mez3, two of the three putative H3K27me3 methyltranferases present in the maize genome, suggests partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 requires Mez2 and/or Mez3 and there was limited evidence for functional consequences of H3K27me3 at these targets. This study provides a catalogue of 6,337 genes that are marked by H3K27me3 in five maize tissues.

Data files

Browseable data files formatted for the Broad Institute's Integrated Genomics Viewer are presented here:

To use these files:

  1. Navigate to the IGV start page (
  2. Launch the IGV with 2 GB RAM
  3. Set the genome to Maize (ZmB73 5a) which will use the AGPv2 coordinate set
  4. Select File...Load from URL and paste in the URL for any of the data tracks you wish to browse. You can determine the URL by right-clicking on the link on this page and choosing Copy Link Location/Copy URL/etc in your browser.
  5. Alternatively, you can download the files to disk and interact with them locally. However, these files can be quite large!
  6. When you have set up the view in the IGV Browser to your liking, you can save the session by choosing File...Save Session. When you launch the browser next time, you will be able to use the resulting XML file to restore your view.

Original data

The original data files for this experiment will be available via NCBI SRA upon publication