What is the relation between transposable elements and methylation?

For purposes of proposal and reports, I have gone back to look at a small project done in collaboration with scientist at IFREMER looking at pesticide exposure on oyster larvae methylation. 

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The control library had limited yield so the number of loci with data from the treated and the control library was restricted. However using a liberal 3x coverage for both, we found a total of 823 DMRs (544 hypermethylated and 279 hypomethylated). 

![igv](http://eagle.fish.washington.edu/cnidarian/skitch/IGV_-_Session___Volumes_web_halfshell_2015-05-comgenbro_igv_session_xml_1B4EF52B.png)

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Intriguingly, when one accounts for all CGs in the genome, these DMRs are predominantly in transposable elements.

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_7_9_15__11_15_AM_1B4EF5A5.png" alt="Screenshot_7_9_15__11_15_AM_1B4EF5A5.png"/>

Reminiscent of ...

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/biorxiv_org_content_biorxiv_early_2015_03_13_012831_full_pdf_1B4EF6FD.png" alt="biorxiv_org_content_biorxiv_early_2015_03_13_012831_full_pdf_1B4EF6FD.png"/>

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The analysis is not pretty, but here is what I have to offer.
https://github.com/sr320/nb-2015/blob/master/Cg/YE-pesticide/YE-pesticide-summary.ipynb