<P> The structural basis for binding of RNA to the argonaute protein was examined by X-ray crystallography of the binding domain of an RNA - bound argonaute protein . Here, the phosphorylated 5' end of the RNA strand enters a conserved basic surface pocket and makes contacts through a divalent cation (an atom with two positive charges) such as magnesium and by aromatic stacking (a process that allows more than one atom to share an electron by passing it back and forth) between the 5' nucleotide in the siRNA and a conserved tyrosine residue . This site is thought to form a nucleation site for the binding of the siRNA to its mRNA target . Analysis of the inhibitory effect of mismatches in either the 5' or 3' end of the guide strand has demonstrated that the 5' end of the guide strand is likely responsible for matching and binding the target mRNA, while the 3' end is responsible for physically arranging target mRNA into a cleavage - favorable RISC region . </P> <P> It is not understood how the activated RISC complex locates complementary mRNAs within the cell . Although the cleavage process has been proposed to be linked to translation, translation of the mRNA target is not essential for RNAi - mediated degradation . Indeed, RNAi may be more effective against mRNA targets that are not translated . Argonaute proteins are localized to specific regions in the cytoplasm called P - bodies (also cytoplasmic bodies or GW bodies), which are regions with high rates of mRNA decay; miRNA activity is also clustered in P - bodies . Disruption of P - bodies decreases the efficiency of RNA interference, suggesting that they are a critical site in the RNAi process . </P> <P> Components of the RNAi pathway are used in many eukaryotes in the maintenance of the organization and structure of their genomes . Modification of histones and associated induction of heterochromatin formation serves to downregulate genes pre-transcriptionally; this process is referred to as RNA - induced transcriptional silencing (RITS), and is carried out by a complex of proteins called the RITS complex . In fission yeast this complex contains argonaute, a chromodomain protein Chp1, and a protein called Tas3 of unknown function . As a consequence, the induction and spread of heterochromatic regions requires the argonaute and RdRP proteins . Indeed, deletion of these genes in the fission yeast S. pombe disrupts histone methylation and centromere formation, causing slow or stalled anaphase during cell division . In some cases, similar processes associated with histone modification have been observed to transcriptionally upregulate genes . </P> <P> The mechanism by which the RITS complex induces heterochromatin formation and organization is not well understood . Most studies have focused on the mating - type region in fission yeast, which may not be representative of activities in other genomic regions / organisms . In maintenance of existing heterochromatin regions, RITS forms a complex with siRNAs complementary to the local genes and stably binds local methylated histones, acting co-transcriptionally to degrade any nascent pre-mRNA transcripts that are initiated by RNA polymerase . The formation of such a heterochromatin region, though not its maintenance, is dicer - dependent, presumably because dicer is required to generate the initial complement of siRNAs that target subsequent transcripts . Heterochromatin maintenance has been suggested to function as a self - reinforcing feedback loop, as new siRNAs are formed from the occasional nascent transcripts by RdRP for incorporation into local RITS complexes . The relevance of observations from fission yeast mating - type regions and centromeres to mammals is not clear, as heterochromatin maintenance in mammalian cells may be independent of the components of the RNAi pathway . </P>

The process of rna interference has been used in the development of plants resistant to