Editing Small interfering RNA (section)

== Post-transcriptional gene silencing ==
The siRNA-induced post transcriptional gene silencing is initiated by the assembly of the [[RNA-induced silencing complex]] (RISC). The complex silences certain gene expression by cleaving the mRNA molecules coding the target genes. To begin the process, one of the two siRNA strands, the guide strand (anti-sense strand), will be loaded into the RISC while the other strand, the passenger strand (sense strand), is degraded. Certain Dicer enzymes may be responsible for loading the guide strand into RISC.<ref>{{cite journal | vauthors = Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, Carthew RW | title = Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways | journal = Cell | volume = 117 | issue = 1 | pages = 69–81 | date = April 2004 | pmid = 15066283 | doi = 10.1016/s0092-8674(04)00261-2 | s2cid = 6683459 | doi-access = free }}</ref> Then, the siRNA scans for and directs RISC to perfectly complementary sequence on the mRNA molecules.<ref name=pmid19239886>{{cite journal | vauthors = Carthew RW, Sontheimer EJ | title = Origins and Mechanisms of miRNAs and siRNAs | journal = Cell | volume = 136 | issue = 4 | pages = 642–55 | date = February 2009 | pmid = 19239886 | pmc = 2675692 | doi = 10.1016/j.cell.2009.01.035 }}</ref> The cleavage of the mRNA molecules is thought to be catalyzed by the Piwi domain of [[Argonaute]] proteins of the RISC. The mRNA molecule is then cut precisely by cleaving the phosphodiester bond between the target nucleotides which are paired to siRNA residues 10 and 11, counting from the 5'end.<ref name=pmid15741316>{{cite journal | vauthors = Tomari Y, Zamore PD | title = Perspective: machines for RNAi | journal = Genes & Development | volume = 19 | issue = 5 | pages = 517–29 | date = March 2005 | pmid = 15741316 | doi = 10.1101/gad.1284105 | doi-access = free }}</ref> This cleavage results in mRNA fragments that are further degraded by cellular [[exonuclease]]s. The 5' fragment is degraded from its [[Directionality (molecular biology)|3' end]] by [[Exosome complex|exosome]] while the 3' fragment is degraded from its [[Directionality (molecular biology)|5' end]] by 5' -3' exoribonuclease 1([[5'-3' exoribonuclease 1|XRN1]]).<ref>{{cite journal | vauthors = Orban TI, Izaurralde E | title = Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome | journal = RNA | volume = 11 | issue = 4 | pages = 459–69 | date = April 2005 | pmid = 15703439 | pmc = 1370735 | doi = 10.1261/rna.7231505 }}</ref> Dissociation of the target mRNA strand from RISC after the cleavage allow more mRNA to be silenced. This dissociation process is likely to be promoted by extrinsic factors driven by [[ATP hydrolysis]].<ref name=pmid15741316/>

Sometimes cleavage of the target mRNA molecule does not occur. In some cases, the endonucleolytic cleavage of the phosphodiester backbone may be suppressed by mismatches of siRNA and target mRNA near the cleaving site. Other times, the Argonaute proteins of the RISC lack [[endonuclease]] activity even when the target mRNA and siRNA are perfectly paired.<ref name=pmid15741316/> In such cases, gene expression will be silenced by an miRNA induced mechanism instead <ref name=pmid19239886/>
[[File:The Ping-Pong Method.png|thumb|A simplified version of the Ping-Pong Method, involving proteins Aubergine (Aub) and Argonaute-3 (Ago3) cleaving the 3' and 5' ends of piRNA.]]<ref name="pmid28696921"/>

[[Piwi-interacting RNA]]s are responsible for the silencing of transposons and are not siRNAs.<ref name="pmid30446728">{{cite journal | vauthors=Ozata DM, Gainetdinov I, Zoch A, Phillip D, Zamore PD | title=PIWI-interacting RNAs: small RNAs with big functions | journal=[[Nature Reviews Genetics]] | volume=20 | issue=2 | pages=89–108 | year=2019 | doi = 10.1038/s41576-018-0073-3| pmid=30446728| s2cid=53565676 | url=https://www.pure.ed.ac.uk/ws/files/78781529/PIWI_interacting_RNAs_AAM_zata_et_al._Revised_v2.3.pdf }}</ref> PIWI-interacting RNAs (piRNAs) are a recently-discovered class of small non-coding RNAs (ncRNAs) with a length of 21-35 nucleotides. They play a role in gene expression regulation, transposon silencing, and viral infection inhibition. Once considered as "dark matter" of ncRNAs, piRNAs emerged as important players in multiple cellular functions in different organisms.<ref name="pmid32655289">{{cite journal | vauthors= Monga I, Banerjee I | title=Computational Identification of piRNAs Using Features Based on RNA Sequence, Structure, Thermodynamic and Physicochemical Properties | journal=[[Current Genomics]] | volume=20 | issue=2 | pages=508–518 | year=2019 | doi = 10.2174/1389202920666191129112705| pmid=32655289|url=https://www.eurekaselect.com/177061/article | pmc=7327968 }}</ref>

=== Transcriptional Gene Silencing ===
Many model organism, such as plants ([[Arabidopsis thaliana]]), yeast ([[Saccharomyces cerevisiae  ]]), flies ([[Drosophila melanogaster]]) and worms ([[C. elegans]]), have been used to study small non coding RNA-directed Transcriptional gene silencing. In human cell, RNA-directed transcriptional gene silencing was observed a decade ago when exogenous siRNAs silenced a transgenic elongation factor 1 α promoter driving a [[Green Fluorescent Protein]] (GFP) reporter gene.<ref name="ncbi.nlm.nih.gov">{{cite journal |last1=Marc S |first1=Weinberg |last2=Kevin V |first2=Morris |title=Transcriptional gene silencing in humans |journal=Nucleic Acids Research |date=Aug 2016 |volume=44 |issue=14 |pages=6505–6517 |doi=10.1093/nar/gkw139 |pmid=27060137 |pmc=5001580 |doi-access=free }}</ref>
The main mechanisms of transcriptional gene silencing (TGS) involving the RNAi machinery include DNA methylation, histone [[post-translational modifications]], and subsequent [[chromatin remodeling]] around the target gene into a heterochromatic state.<ref name="ncbi.nlm.nih.gov"/>
SiRNAs can be incorporated into a [[RNA-induced transcriptional silencing]] (RITS) complex. An active RITS complex will trigger the formation of [[heterochromatin]] around DNA matching the siRNA, effectively silencing the genes in that region of the DNA.