Variation in DNA methylation patterns more common among maize inbreds than among tissues

Original manuscript: http://www.crops.org/publications/tpg/abstracts/0/0/plantgenome2012.06.0009

Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize.

Data files

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

RNAseq summary files for B73 amd Mo17 tissues:

To use these files:

  1. Navigate to the IGV start page (http://www.broadinstitute.org/software/igv/StartIGV)
  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 can be found at NCBI GEO under accession GSE33730.