RNA-Directed DNA Methylation

RNA-directed DNA methylation (RdDM) is an epigenetic process first discovered in plants (Wassenegger et al, 1994, Cell, Vol 76, 567-576). During RdDM, double-stranded RNAs (dsRNAs) are processed to 21-24 nucleotide small interfering RNAs (siRNAs) and guide methylation of homologous DNA loci. In plants dsRNAs may be generated from three sources:

• Viral replication intermediates
• Products of the endogenous RNA-directed RNA polymerase
• Transcribed inverted repeats

Besides RNA molecules, a plethora of proteins are involved in the establishment of RdDM, like Argonautes, DNA methyltransferases, chromatin remodelling complexes and the plant-specific PolIV and PolV. All these act in concert to add a methyl-group at the 5' position of cytosines. In contrast to animals, cytosines at all sequence context (CG, CHG, CHH) may get de novo methylated in plants.

References

• Wassenegger, Michael; Heimes, Sabine; Riedel, Leonhard; Sänger, Heinz L. (1994). "RNA-directed de novo methylation of genomic sequences in plants". Cell 76 (3): 567–76. doi:10.1016/0092-8674(94)90119-8. PMID 8313476. 
• Law, Julie A.; Jacobsen, Steven E. (2010). "Establishing, maintaining and modifying DNA methylation patterns in plants and animals". Nature Reviews Genetics 11 (3): 204–20. doi:10.1038/nrg2719. PMC 3034103. PMID 20142834. 
• Haag, Jeremy R.; Pikaard, Craig S. (2011). "Multisubunit RNA polymerases IV and V: Purveyors of non-coding RNA for plant gene silencing". Nature Reviews Molecular Cell Biology 12 (8): 483–92. doi:10.1038/nrm3152. PMID 21779025. 
• Bender, Judith (2012). "RNA-Directed DNA Methylation: Getting a Grip on Mechanism". Current Biology 22 (10): R400–1. doi:10.1016/j.cub.2012.04.010. PMID 22625855. 
• Dalakouras, Athanasios; Wassenegger, Michael (2013). "Revisiting RNA-directed DNA methylation". RNA Biology 10 (3): 453–5. doi:10.4161/rna.23542. PMC 3672289. PMID 23324611.