@article{9506,
  abstract     = {Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.},
  author       = {Zilberman, Daniel},
  issn         = {1465-6906},
  journal      = {Genome Biology},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{An evolutionary case for functional gene body methylation in plants and animals}},
  doi          = {10.1186/s13059-017-1230-2},
  volume       = {18},
  year         = {2017},
}

@article{9514,
  abstract     = {Background:
DNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.
Results:
We used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.
Conclusion:
We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.},
  author       = {Tran, Robert K. and Zilberman, Daniel and de Bustos, Cecilia and Ditt, Renata F. and Henikoff, Jorja G. and Lindroth, Anders M. and Delrow, Jeffrey and Boyle, Tom and Kwong, Samson and Bryson, Terri D. and Jacobsen, Steven E. and Henikoff, Steven},
  issn         = {1465-6906},
  journal      = {Genome Biology},
  number       = {11},
  publisher    = {Springer Nature},
  title        = {{Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis}},
  doi          = {10.1186/gb-2005-6-11-r90},
  volume       = {6},
  year         = {2005},
}

@article{9511,
  abstract     = {Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it.},
  author       = {Zilberman, Daniel and Henikoff, Steven},
  issn         = {1465-6906},
  journal      = {Genome Biology},
  number       = {12},
  publisher    = {Springer Nature},
  title        = {{Silencing of transposons in plant genomes: kick them when they're down}},
  doi          = {10.1186/gb-2004-5-12-249},
  volume       = {5},
  year         = {2004},
}