The length of siRNA is 21-25 bp, they are formed from dsRNA. The source of such RNAs can be viral infections, genetic constructs introduced into the genome, long hairpins in transcripts, and bidirectional transcription of mobile elements.
dsRNA is cut by RNase Dicer into fragments 21-25 bp long. with 3" ends protruding by 2 nucleotides, after which one of the chains is part of RISC and directs the cutting of homologous RNAs. RISC contains siRNAs corresponding to both plus and minus strands of dsRNA. siRNAs do not have their own genes and represent are fragments of longer RNAs. siRNAs direct the cutting of the target RNA, since they are completely complementary to it. In plants, fungi and nematodes, RNA-dependent RNA polymerases are involved in the process of suppressing gene expression, for which siRNAs also serve as primers (seeds for the synthesis of new RNA The resulting dsRNA is cut by Dicer, new siRNAs are formed, which are secondary, thus amplifying the signal. 
RNA interference
In 1998, Craig C. Mello and Andrew Fire published in Nature, which stated that double-stranded RNA (dsRNA) is capable of repressing gene expression. Later it turned out that the active principle in this process is short single-stranded RNA. The mechanism of suppression of gene expression using these RNAs is called
RNA interference, as well as RNA silencing. This mechanism is found in all large taxa of eukaryotes: vertebrates and invertebrates, plants and fungi. In 2006, he received the Nobel Prize for this discovery.
Suppression of expression can occur at the transcriptional level or post-transcriptionally. It turned out that in all cases a similar set of proteins and short (21-32 bp) RNAs are required.
siRNAs regulate gene activity in two ways. As mentioned above, they direct the cutting of target RNAs. This phenomenon is called "suppression" ( quelling) in mushrooms, " post-translational gene silencing"in plants and" RNA interference
"in animals. siRNAs 21-23 bp long are involved in these processes. Another type of effect is that siRNAs can suppress the transcription of genes containing homologous siRNA sequences. This phenomenon was called transcriptional gene silencing
(TGS) and is found in yeast, plants and animals. siRNAs also direct DNA methylation, which leads to heterochromatin formation and transcriptional repression. TGS is best studied in the yeast S. pombe, where siRNAs are found to be integrated into a RISC-like protein complex called RITS. In his case, as in the case of RISC, siRNA interacts with a protein of the AGO family. It is likely that siRNA is able to direct this complex to a gene that contains a homologous siRNA fragment. After this, RITS proteins recruit methyltransferases, as a result of which heterochromatin is formed in the locus encoding the siRNA target gene, and active gene expression ceases. 
Role in cellular processes
What is the significance of siRNA in a cell?
siRNAs are involved in cell protection from viruses, repression of transgenes, regulation of certain genes, and formation of centromeric heterochromatin. Important Feature siRNA suppression of the expression of mobile genetic elements. Such suppression can occur both at the transcriptional level and posttranscriptionally.
The genome of some viruses consists of DNA, while others consist of RNA, and the RNA of viruses can be either single- or double-stranded. The process of cutting foreign (viral) mRNA in this case occurs in the same way as described above, that is, by activating the RISC enzyme complex. However, for greater efficiency, plants and insects have invented a unique way to enhance the protective effect of siRNA. By joining the mRNA strand, a section of siRNA can, with the help of the DICER enzyme complex, first complete the second strand of mRNA and then cut it in different places, thus creating a variety of “secondary” siRNAs. They, in turn, form RISC and carry the mRNA through all the stages discussed above, up to its complete destruction. Such “secondary” molecules will be able to specifically bind not only to the part of the viral mRNA to which the “primary” molecule was directed, but also to other areas, which dramatically increases the effectiveness of cellular defense.
Thus, in plants and lower animal organisms, siRNAs are an important part of a kind of “intracellular immunity” that allows them to recognize and quickly destroy foreign RNA. If an RNA containing a virus has entered the cell, such a protection system will prevent it from multiplying. If the virus contains DNA, the siRNA system will prevent it from producing viral proteins (since the necessary mRNA for this will be recognized and cut), and using this strategy will slow down its spread throughout the body.
Mammals, unlike insects and plants, have a different defense system. When foreign RNA, the length of which is more than 30 bp, enters a “mature” (differentiated) mammalian cell, the cell begins to synthesize interferon. Interferon, by binding to specific receptors on the cell surface, is able to stimulate a whole group of genes in the cell. As a result, several types of enzymes are synthesized in the cell, which inhibit protein synthesis and break down viral RNA. In addition, interferon can also act on neighboring, not yet infected cells, thereby blocking the possible spread of the virus.
As you can see, both systems are similar in many ways: they have a common goal and “methods” of work. Even the names “interferon” and “(RNA) interference” themselves come from a common root. But they also have one very significant difference: if interferon, at the first signs of invasion, simply “freezes” the work of the cell, not allowing (just in case) the production of many, including “innocent” proteins in the cell, then the siRNA system is extremely intelligible : Each siRNA will recognize and destroy only its own specific mRNA. Replacement of just one nucleotide within siRNA leads to a sharp decrease in the interference effect . None of the gene blockers known so far has such exceptional specificity for its target gene.
The discovery of RNA interference has given new hope in the fight against AIDS and cancer. It is possible that by using siRNA therapy along with traditional antiviral therapy, a potentiation effect can be achieved, where the two treatments result in a greater therapeutic effect than the simple sum of each given separately.
In order to use the siRNA interference mechanism in mammalian cells, ready-made double-stranded siRNA molecules must be introduced into the cells. The optimal size of such synthetic siRNA is the same 21-28 nucleotides. If you increase its length, the cells will respond by producing interferon and reducing protein synthesis. Synthetic siRNAs can enter both infected and healthy cells, and a decrease in protein production in uninfected cells would be highly undesirable. On the other hand, if you try to use siRNA smaller than 21 nucleotides, the specificity of its binding to the desired mRNA and the ability to form the RISC complex sharply decrease.
If it is possible to deliver siRNA in one way or another that has the ability to bind to any part of the HIV genome (which, as is known, consists of RNA), one can try to prevent its integration into the DNA of the host cell. In addition, scientists are developing ways to influence various stages of HIV reproduction in an already infected cell. The latter approach will not provide a cure, but it can significantly reduce the rate of virus reproduction and give the cornered immune system a chance to “rest” from the viral attack and try to deal with the remnants of the disease itself. In the figure, the two stages of HIV reproduction in a cell, which scientists hope can be blocked using siRNA, are marked with red crosses (stages 4-5 - integration of the virus into the chromosome, and stages 5-6 - assembly of the virus and exit from the cell). 
Today, however, all of the above relates only to the field of theory. In practice, siRNA therapy encounters difficulties that scientists have not yet been able to overcome. For example, in the case of antiviral therapy, it is the high specificity of siRNA that can play a cruel joke: as is known, viruses have the ability to quickly mutate, i.e. change the composition of its nucleotides. HIV has been especially successful in this, the frequency of changes in which is such that a person infected with one subtype of the virus can, after a few years, develop a completely different subtype. In this case, the modified HIV strain will automatically become insensitive to the siRNA selected at the beginning of therapy.
Aging and carcinogenesis
Like any epigenetic factor, siRNAs affect the expression of genes that are silenced. Now there are works that describe experiments on switching off genes associated with tumors. Genes are switched off (knock-down) using siRNA. For example, Chinese scientists used siRNA to turn off the transcription factor 4 (TCF4) gene, whose activity causes Pitt-Hopkins syndrome (a very rare genetic disease characterized by mental retardation and episodes of hyperventilation and apnea) and other mental diseases. In this work, we studied the role of TCF4 in gastric cancer cells. Ectopic expression of TCF4 reduces cell growth in gastric cancer cell lines, knocking out the TCF4 gene using siRNA increases cell migration. Thus, we can conclude that epigenetic switching off (silencing) of the TCF4 gene plays an important role in the formation and development of tumors.
According to research in the Department of Oncology, Albert Einstein Cancer Center, led by Leonard H. Augenlicht, siRNA is involved in turning off the HDAC4 gene, which causes inhibition of colon cancer growth, apoptosis and increased transcription of p21. HDAC4 is a histone deacetylase that is tissue specific, inhibits cell differentiation, and its expression is suppressed during the process of cell differentiation. The work shows that HDAC4 is an important regulator of colon cell proliferation (which is important in the cancer process), and it, in turn, is regulated by siRNA.
The Department of Pathology, Nara Medical University School of Medicine in Japan conducted research on prostate cancer. Replicative cell aging is a barrier against uncontrolled division and carcinogenesis. Short-lived dividing cells (TAC) are part of the prostate cell population from which tumors form. Japanese scientists studied the reasons why these cells overcome aging. Prostate cells in culture were transfected with junB siRNA. These cells exhibit increased expression levels of p53, p21, p16 and pRb, which are detected during aging. Cells in culture that showed reduced levels of p16 were used for the next step. Repeated siRNA transfection into TAC allowed cells to avoid senescence upon p16/pRb inactivation. In addition, silencing of the junB proto-oncogene by junB siRNA causes cell invasion. Based on this, it was concluded that junB is an element for p16 and promotes cellular senescence, preventing TAC malignancy. Thus, junB is a regulator of prostate carcinogenesis and may be a target for therapeutic intervention. And its activity can be regulated using siRNA.
There are a lot of similar studies being carried out. Currently, siRNA is not only an object, but also a tool in the hands of a researcher - doctor, biologist, oncologist, gerontologist. Studying the connection between siRNA and cancer and the expression of age-associated genes is the most important task for science. Very little time has passed since the discovery of siRNA, but many interesting studies and publications related to them have appeared. There is no doubt that their study will be one of humanity’s steps towards victory over cancer and aging...
), preventing the translation of mRNA on ribosomes into the protein it encodes. Ultimately, the effect of small interfering RNA is identical to that of simply reducing gene expression.
Small interfering RNAs were discovered in 1999 by David Baulcombe's group in the UK as a component of a post-transcriptional gene silencing system in plants. PTGS, en:post-transcriptional gene silencing). The team published their findings in the journal Science.
Double-stranded RNA can enhance gene expression through a mechanism called RNA-dependent gene activation. RNAa, small RNA-induced gene activation). It has been shown that double-stranded RNAs complementary to the promoters of target genes cause activation of the corresponding genes. RNA-dependent activation upon administration of synthetic double-stranded RNA has been demonstrated for human cells. It is not known whether a similar system exists in the cells of other organisms.
By providing the ability to turn off essentially any gene at will, small interfering RNA-based RNA interference has generated enormous interest in basic and applied biology. The number of broad-based RNAi-based tests to identify important genes in biochemical pathways is growing. Since the development of diseases is also determined by the activity of genes, it is expected that in some cases, switching off a gene using small interfering RNA may have a therapeutic effect.
However, the application of small interfering RNA-based RNA interference to animals, and especially to humans, faces many difficulties. Experiments have shown that the effectiveness of small interfering RNA is different for different types cells: some cells readily respond to small interfering RNA and demonstrate a decrease in gene expression, while in others this is not observed, despite effective transfection. The reasons for this phenomenon are still poorly understood.
Results from phase 1 trials of the first two RNAi therapeutics (intended to treat macular degeneration), published in late 2005, show that small interfering RNA drugs are easily tolerated by patients and have acceptable pharmacokinetic properties.
Preliminary clinical trials of small interfering RNAs targeting the Ebola virus indicate that they may be effective for post-exposure prophylaxis of the disease. This drug allowed the entire group of experimental primates to survive after receiving a lethal dose of the Zaire Ebolavirus
Scientists believe that incorrect expression of small RNAs is one of the causes of a number of diseases that seriously affect the health of many people around the world. These diseases include cardiovascular 23 and cancer 24 . As for the latter, this is not surprising: cancer indicates anomalies in the development of cells and their fate, and small RNAs play vital role in the relevant processes. Here is one of the very illustrative examples the enormous impact that small RNAs have on the body during cancer. It's about about a malignant tumor, which is characterized by incorrect expression of those genes that act during the initial development of the organism, and not in the postnatal period. This is a type of childhood brain tumor that usually appears before the age of two. Unfortunately, this is a very aggressive form of cancer, and the prognosis here is unfavorable even with intensive treatment. The oncological process develops due to improper redistribution genetic material in brain cells. A promoter that normally drives strong expression of one of the protein-coding genes undergoes recombination with a specific cluster of small RNAs. Then this entire rearranged region undergoes amplification: in other words, many copies of it are created in the genome. Consequently, small RNAs located “downstream” of the relocated promoter are expressed much more strongly than they should be. The level of active small RNAs is approximately 150-1000 times higher than normal.
Rice. 18.3. Small RNAs activated by alcohol can combine with messenger RNAs that do not affect the body's resistance to the effects of alcohol. But these small RNAs do not bind to the messenger RNA molecules that promote such resistance. This results in a relative predominance of the proportion of messenger RNA molecules encoding protein variations associated with alcohol tolerance.
This cluster encodes more than 40 different small RNAs. In fact, this is generally the largest of such clusters found in primates. It is usually expressed only at an early stage human development, in the first 8 weeks of embryonic life. Its strong activation in the infant brain leads to catastrophic effects on genetic expression. One consequence is the expression of an epigenetic protein that adds modifications to the DNA. This leads to widespread changes in the entire pattern of DNA methylation, and therefore to abnormal expression of all sorts of genes, many of which should be expressed only when immature brain cells divide during early stages development of the body. This is how the cancer program starts in the baby's cells 25.
Such communication between small RNAs and the epigenetic machinery of the cell can have a significant impact on other situations when cells develop a predisposition to cancer. This mechanism likely results in the effect of disruption of small RNA expression being enhanced by changes in epigenetic modifications that are transmitted to daughter cells from the mother. This can create a pattern of potentially dangerous changes in the pattern of gene expression.
So far, scientists have not figured out all the stages of the interaction of small RNAs with epigenetic processes, but they can still get some hints about the features of what is happening. For example, it turned out that a certain class of small RNAs, which enhance the aggressiveness of breast cancer, targets certain enzymes in messenger RNAs that remove key epigenetic modifications. This alters the pattern of epigenetic modifications in the cancer cell and further disrupts genetic expression 26 .
Many forms of cancer are difficult to track in a patient. Oncological processes can occur in hard-to-reach places, which complicates the sampling procedure. In such cases, it is not easy for the doctor to monitor the development of the cancer process and the response to treatment. Often doctors are forced to rely on indirect measurements - say, a tomographic scan of a tumor. Some researchers believe that small RNA molecules could help create a new technique for monitoring tumor development, which could also study its origin. When cancer cells die, small RNAs leave the cell when it ruptures. These small junk molecules often form complexes with cellular proteins or are wrapped in fragments cell membranes. Due to this, they are very stable in body fluids, which means that such RNAs can be isolated and analyzed. Since their quantities are small, researchers will have to use very sensitive analysis methods. However, nothing is impossible here: the sensitivity of nucleic acid sequencing is constantly increasing 27 . Data have been published confirming the promise of this approach for breast cancer 28 , ovarian cancer 29 and a number of other cancers. Analysis of small circulating RNAs in lung cancer patients has shown that these RNAs help distinguish between patients with a solitary pulmonary nodule (not requiring therapy) and patients who develop malignant tumor nodules (requiring treatment) 30 .
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small nuclear (low molecular weight nuclear) RNAs- An extensive group (105,106) of small nuclear RNAs (100,300 nucleotides), associated with heterogeneous nuclear RNA, are part of small ribonucleoprotein granules of the nucleus; M.n.RNAs are a necessary component of the splicing system... ...
small cytoplasmic RNAs- Small (100-300 nucleotide) RNA molecules localized in the cytoplasm, similar to small nuclear RNA. [Arefyev V.A., Lisovenko L.A. English Russian Dictionary genetic terms 1995 407 pp.] Topics genetics EN scyrpssmall cytoplasmic... ... Technical Translator's Guide
class U small nuclear RNAs- A group of protein-associated small (from 60 to 400 nucleotides) RNA molecules that make up a significant part of the contents of the splicome and are involved in the process of excision of introns; in 4 of the 5 well-studied Usn types, U1, U2, U4 and U5 RNAs are 5... ... Technical Translator's Guide
RNA biomarkers- * RNA biomarkers * RNA biomarkers a huge number of human transcripts that do not encode protein synthesis (nsbRNA or npcRNA). In most cases, small (miRNA, snoRNA) and long (antisense RNA, dsRNA and other types) RNA molecules are... ... Genetics. encyclopedic Dictionary
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