Spreading of heterochromatin is limited to specific families of maize retrotransposons

Original manuscript: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003127

Transposable elements comprise a substantial portion of many eukaryotic genomes. These mobile fragments of DNA can directly mutate genes through insertions into coding regions but may also affect the gene regulation through nearby insertions. There is evidence that the majority of transposable elements are epigenetically silenced and in some cases this silencing may spread to neighboring sequences. This spreading of heterochromatin could create a significant fitness tradeoff between transposon silencing and gene expression. The maize genome has a complex organization with many genes flanked by retrotransposons providing an opportunity to study the interaction of retrotransposons and genes. To survey the prevalence of heterochromatin spreading associated with different retrotransposon families we profiled the spread of heterochromatin into nearby low copy sequences for 150 high copy retrotransposon families. While many retrotransposons exhibit little to no spreading of heterochromatin, there are some retrotransposon families that do exhibit spreading. The families may represent bad “neighbors” that spread heterochromatin and suppress expression of nearby genes. Consistent with this idea, the genes located near retrotransposons with heterochromatin spreading have lower expression levels.

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 TBD.