Epigenetic and genetic influences on DNA methylation variation in maize populations
Original manuscript: http://www.plantcell.org/content/early/2013/08/02/tpc.113.114793.full.pdf+html
DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, there is also evidence that genetic changes such as transposon insertions can lead to changes in DNA methylation levels. Genome-wide profiles of DNA methylation levels for 20 maize inbreds were used to discover differentially methylated regions (DMRs). The methylation levels for each of these DMRs were also assayed in 31 additional maize genotypes resulting in the discovery of 1,966 common DMRs and 1,754 rare DMRs. The analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with SNPs found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the DNA methylation variation. The analysis of gene expression in the same samples used for DNA methylation profiling identifies over 300 genes with expression patterns that are significantly associated with the DNA methylation variation among genotypes. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic variation, is often stably inherited and can influence expression level of genes in the population
Browseable data files formatted for the Broad Institute's Integrated Genomics Viewer are presented here:
- 51 genos meDIP (386 MB .igv)
- 51 genos meDIP (242 MB .tdf)
- Segment file for 9899 DMRs across 51 genos (21 MB .seg)
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 ....