RNA-directed DNA methylation (RdDM) is an epigenetic

Epigenetics

In biology, and specifically genetics, epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence – hence the name epi- -genetics...

 process first elucidated in plants whereby small double-stranded RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

s (dsRNA's) are processed to guide methylation

Methylation

In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...

 to complementary DNA loci

Locus (genetics)

In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...

. In the model plant organism Arabidopsis thaliana, these small dsRNA's may be generated from three sources:

• Viral replication
  Viral replication
  Viral replication is the term used by virologists to describe the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. From the perspective of the virus, the purpose of viral replication is...
  
   intermediates
• Products of the endogenous RNA-dependent RNA polymerase
  RNA polymerase
  RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
  
  
• Transcribed inverted repeats

These dsRNAs are then processed to direct histone 3 lysine 9 (H3K9) methylation via Ago4 and the SUVH (Suppressor of Variegation Homolog) histone methyltransferase

Histone methyltransferase

Histone methyltransferases are enzymes, histone-lysine N-methyltransferase and histone-arginine N-methyltransferase, that catalyze the transfer of one to three methyl groups from the cofactor S-Adenosyl methionine to lysine and arginine residues of histone proteins...

 family. This H3K9 dimethylation is then putatively bound by the cytosine

Cytosine

Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...

 methyltransferase CMT3, which methylates cytosines in a non-CG context.

These marks, H3K9 dimethylation and cytosine methylation, are canonical marks of gene silencing

Gene silencing

Gene silencing is a general term describing epigenetic processes of gene regulation. The term gene silencing is generally used to describe the "switching off" of a gene by a mechanism other than genetic modification...

. Thus small double stranded RNAs generated in diverse contexts bring about transcriptional silencing at specific loci.