Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded non-coding RNA molecules, typically 20–24 base pairs in length, similar to microRNA (miRNA), and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading messenger RNA (mRNA) after transcription, preventing translation. It was discovered in 1998 by Andrew Fire at the Carnegie Institution for Science in Washington, D.C. and Craig Mello at the University of Massachusetts in Worcester.

Structure

Naturally occurring siRNAs have a well-defined structure that is a short (usually 20 to 24-bp) double-stranded RNA (dsRNA) with phosphorylated 5' ends and hydroxylated 3' ends with two overhanging nucleotides. As of 2001, it had been suggested that an enzyme referred to as Dicer catalyzed "the initiation step of RNA interference" (production of siRNAs from long dsRNAs and small hairpin RNAs).

siRNAs can also be introduced into cells by transfection. Since, in principle, any gene can be knocked down by a synthetic siRNA with a complementary sequence, siRNAs are an important tool for validating gene function and drug targeting in the "post-genomic era".

History

In 1998, Andrew Fire at Carnegie Institution for Science in Washington DC and Craig Mello at University of Massachusetts in Worcester discovered the RNAi mechanism while working on gene expression in the nematode, Caenorhabditis elegans. The two won the Nobel prize for their research with RNAi in 2006. siRNA and its role in post-transcriptional gene silencing (PTGS) was discovered in plants by David Baulcombe's group at the Sainsbury Laboratory in Norwich, England, a discovery reported in Science in 1999. Primary sources cannot establish first-to-discover history. Thomas Tuschl and colleagues soon reported in Nature that synthetic siRNAs could induce RNAi in mammalian cells. Primary sources cannot establish first-to-discover history. These discoveries led to a surge in interest in harnessing RNAi for biomedical research and drug development.

As of 2017, human applications of siRNA had faced significant roadblocks to their success, one of these being "off-targeting". As that decade came to a close, the possibility that these therapies could trigger innate immunity had been discussed. As of 2019, animal models had not been successful in accurately representing the extent of this response in humans; hence, studying the effects of siRNA therapies has been a challenge.

As of 2025, seven siRNA-based drugs have received approval from the U.S. Food and Drug Administration (FDA), spanning indications including hypercholesterolaemia, acute hepatic porphyria, primary hyperoxaluria, transthyretin amyloidosis, and haemophilia A and B.

+ FDA-approved siRNA therapeutics (selected) Drug Brand name Patisiran Onpattro Givosiran Givlaari Lumasiran Oxlumo Inclisiran Leqvio Vutrisiran Amvuttra Fitusiran Qfitlia Nedosiran Rivfloza

Mechanism

The mechanism by which natural siRNA causes gene silencing through repression of translation occurs as follows:

Long dsRNA (which can come from hairpin, complementary RNAs, and RNA-dependent RNA polymerases) is cleaved by an endo-ribonuclease called Dicer. Dicer cuts the long dsRNA to form short interfering RNA or siRNA; this is what enables the molecules to form the RNA-Induced Silencing Complex (RISC). Once siRNA enters the cell, it gets incorporated into other proteins to form the RISC. Once the siRNA is part of the RISC complex, the siRNA is unwound to form single-stranded siRNA. The strand that is thermodynamically less stable due to its base pairing at the 5' end is chosen to remain part of the RISC complex. The single-stranded siRNA, which is part of the RISC complex, can now scan and find a complementary mRNA. Once the single-stranded siRNA (part of the RISC complex) binds to its target mRNA, it induces mRNA cleavage. The mRNA is now cut and recognized as abnormal by the cell. This causes degradation of the mRNA and, in turn, no translation of the mRNA into amino acids and then proteins, thus silencing the gene that encodes that mRNA. siRNA is also similar to miRNA; however, miRNAs are derived from shorter stemloop RNA products. miRNAs typically silence genes by repression of translation and have broader specificity of action, while siRNAs typically work with higher specificity by cleaving the mRNA before translation, with 100% complementarity.

RNAi induction using siRNAs or their biosynthetic precursors

Gene knockdown by transfection of exogenous siRNA is only transient, especially in rapidly dividing cells. This may be overcome by creating an expression vector for the siRNA. The siRNA sequence is modified to introduce a short loop between the two strands. The resulting transcript is a short hairpin RNA (shRNA), which can be processed into a functional siRNA by Dicer in its usual fashion. Typical transcription cassettes use an RNA polymerase III promoter (e.g., U6 or H1) to direct the transcription of small nuclear RNAs (snRNAs, where U6 is involved in RNA splicing; H1 is the RNase component of human RNase P). It is theorized that the resulting siRNA transcript is then processed by Dicer.

The gene knockdown efficiency can also be improved by using cell squeezing.

The activity of siRNAs in RNAi is largely dependent on its binding ability to the RNA-induced silencing complex (RISC). Binding of the duplex siRNA to RISC is followed by unwinding and cleavage of the sense strand with endonucleases. The remaining anti-sense strand-RISC complex can then bind to target mRNAs for initiating transcriptional silencing.

RNA activation

In addition to their role in RNAi, siRNAs can also activate gene expression, a phenomenon termed "RNA activation" or RNAa. This was first observed when synthetic siRNAs, termed "small activating RNA" (saRNA), targeting gene promoters were found to induce potent transcriptional activation of target genes. RNAa has been demonstrated to be a conserved mechanism, observed across species from insects, C. elegans, and plants, to mammals (including humans).

The mechanism of RNAa involves the targeting of promoter regions by saRNAs, leading to the recruitment of transcriptional machinery and epigenetic changes that promote gene expression. This process often involves the RNA-induced transcriptional activation (RITA) complex, which includes Argonaute proteins (particularly Ago2), RNA helicase A (RHA), and CTR9. Endogenous miRNAs can also mediate RNAa, expanding the regulatory roles of these small RNAs beyond gene silencing.

Several saRNA-based therapeutics are currently in clinical development. MTL-CEBPA, developed by MiNA Therapeutics, targets the CEBPA gene and is in Phase II trials for liver cancer. RAG-01, developed by Ractigen Therapeutics, targets the p21 gene and is in Phase I trials for non-muscle invasive bladder cancer (NMIBC). These clinical trials represent a significant step towards translating the RNAa phenomenon into novel therapeutic strategies.

Post-transcriptional gene silencing

Richard Carthew et al. state in their 2004 study of siRNA/miRNA silencing pathways in Drosophila that siRNA-induced post-transcriptional gene silencing is initiated by the assembly of the RNA-induced silencing complex (RISC). RISC silences expression of certain genes by cleaving the mRNA molecules coding those genes. To begin the process in that system, they state that one of the two siRNA strands, the anti-sense guide strand, is loaded into the RISC while the other strand, the sense passenger strand, is degraded; they go on to state that certain Drosophila Dicer enzymes may be responsible for loading the guide strand into RISC. Then, in a perspective from 2009, the view is offered that "siRNA scans for and directs RISC" to a perfectly complementary sequence on the mRNA molecules.

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. As Orban and Izaurralde note with regard to a further study in Drosophila cells, "[f]ollowing this initial endonucleolytic cleavage, the mRNA is [further] degraded" by cellular exonucleases; they show that in this system, the 5' fragments "are rapidly degraded from their 3' ends by the exosomes, whereas the 3' fragments are degraded from their 5' ends by XRN1", a 5'-3' exoribonuclease. Dissociation of the target mRNA strand from RISC after the cleavage allows more mRNA to be silenced; this dissociation process is likely to be promoted by extrinsic factors driven by ATP hydrolysis.

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. In such cases, gene expression will be silenced by an miRNA-induced mechanism instead.

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. As stated by Monga and Banerjee in their primary report abstract, "Once considered as 'dark matter' of ncRNAs, piRNAs emerged as important players in multiple cellular functions in different organisms." In particular, as of 2019 they were characterised as not being siRNAs and as being responsible for the silencing of transposons.

Transcriptional gene silencing Many model organisms, 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 cells, RNA-directed transcriptional gene silencing was observed in 2016 when exogenous siRNAs silenced a transgenic elongation factor 1α (EF1a) promoter driving a green fluorescent protein (GFP) reporter gene. 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.

RITS complexes

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.

Applications One of the potent applications of siRNAs is the ability to distinguish the target versus non-target sequence with a single-nucleotide difference. This approach has been considered therapeutically crucial for silencing dominant gain-of-function (GOF) disorders, where the mutant allele causing disease differs from the wild-type allele by a single nucleotide (nt). These types of siRNAs, which are capable of distinguishing a single-nucleotide difference, are termed allele-specific siRNAs.