Heritable Epigenetic Variation among Maize Inbreds
Original manuscript: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002372
Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection.
Browseable data files formatted for the Broad Institute's Integrated Genomics Viewer are presented here:
- B73 MeDIP (24 MB .tdf)
- B73 MeDIP (81 MB .wig)
- Mo17 MeDIP (24 MB .tdf)
- Mo17 MeDIP (81 MB .wig)
- Mo17/B73 CGH (24.3 MB .tdf)
To use these files:
- Navigate to the IGV start page (http://www.broadinstitute.org/software/igv/StartIGV)
- Launch the IGV with 2 GB RAM
- Set the genome to Maize (ZmB73 5a) which will use the AGPv2 coordinate set
- 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.
- Alternatively, you can download the files to disk and interact with them locally. However, these files can be quite large!
- 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.
The original data files for this experiment can be found at NCBI GEO under accession GSE29099.