Upon reflection, I believe that one of the short comings of my prior book on RNA was that I tried too hard to ascribe a mechanism of action to the use of RNA nucleotides. Rather than focusing on the truly vast amount of literature supporting the use of nucleotides and RNA for a huge range of health concerns, I attempted to work from my knowledge of RNA mechanisms to attempt to find a description of how these nucleotides work. While a number of mechanisms are known for RNA in a controlled or laboratory setting, the consensus is that it is still unknown exactly how nucleotides work to achieve their positive results in the body. While nucleotides are reported to have significant effects upon lymphoid, intestinal and hepatic tissues, and lipid metabolism, according to Carver “the mechanism remains unknown” (1995). The American Academy of Pediatrics Committee on Nutrition recognizes the use of nucleotides despite a lack of definitive mode of action. “Currently, nucleotides are added to several infant formulas in the United States. The mechanism by which dietary nucleotides may modify the immune function is unknown, although recent mouse model studies indicate they may augment T helper 1 biased immune responses. Studies in human infants have reported that adding nucleotides to infant formula increases natural killer cell activity, IL2 production b monocytes, serum IgM and IGA concentrations and serum antibody titers.” (Kleinman 2009). Since nucleotides play a role in T lymphocyte development it has been hypothesized this may in part explain their vast positive impacts on the immune system, however it is recognized that “the mechanisms of action of nucleotides on immunity has not been fully clarified” (Norton, 2001).
Similarly, animals supplemented with specific nucleotide blends showed greater resistance to challenges of Staphylococcus aureus and enhanced macrophage phagocyctic activity as compared to control groups. However, “the mechanism of this suppression of nonspecific immunity remains unclear, provision of nucleotides to defined diets appears vital to maintain host resistance to bacterial challenge.” (Kulkarni 1986).
Brunser and colleagues (1994) were able to illustrate a significant decrease in infant diarrheal disease in the nucleotide supplemented group yet were “unable to provide any insights into the potential mechanisms of the reported effects.” Similarly several groups have found a positive impact of nucleotides on lipid profiles in infants. Plasma levels of healthier HDL levels were higher, and troublesome VLDL were lower in nucleotide supplemented groups. However, “the mechanisms have not been elucidated” although the authors suggest that nucleotides may play a regulatory role in lipoprotein regulation via an impact on ACAT activity (1995). Additional research by this group suggests that nucleotides may also play a regulatory role in lipid synthesis in the liver and small intestine (Sanchez-Pozo 2002). Supportive research has reiterated the positive impact on cholesterol with an increase in HDL and lower LDL, “even if the mechanism by which this occurs is still not characterized” (Siahanidou 2004).
What does appear to be known is that specific combinations of nucleotide blends and precise nucleotide ratios do influence the level of positive impact these dietary supplements have in the body.
While the mechanism by which food sources of RNA and DNA nucleotides function is not known, what is known is that the use of RNA over almost fifty years has been proven to have unequivocal effects on healing. A virtual litany of articles exists that cite specific research, which supports the use of nucleotides for a wide variety of health conditions. Much of this work that is cited has its roots in the research of Dr. Benjamin Frank. From the mid 1950’s to the late ‘70s, Dr. Benjamin Frank pioneered the use of nucleic acid in the therapy of aging and chronic diseases. He was able to show that it had profound effects such as: anti-aging, increased energy, anti-anoxia (oxygen sparing), anti-low temperature and freezing, anti-viral and cognitive enhancing activities.
Dr. Frank used RNA for various conditions including atherosclerosis and coronary artery disease. He prescribed a high-dose of nucleic acids (natural RNA and DNA) for atherosclerosis and found that patients had increased exercise tolerance along with decreased shortness of breath with exertion and the disappearance of heart (angina) pains. Congestive Heart Failure (CHF) was also found to have benefited from RNA treatment including the relief of shortness of breath and edema of the legs and ankles. After performing numerous animal experiments, Dr. Frank found that RNA could affect the length of animal survival thus enhancing life span. Nucleic acids or RNA seemed to enhance CoQ10 synthesis, an important energy component in our cells. Subsequent research has demonstrated that supplementation with CoQ10 is useful for a variety of neurological conditions, in particular Parkinson’s disease as well as for congestive heart failure (Shults, CW., Archives of Neurology, Oct, 2002). Dr. Frank also found that RNA supplementation resulted in increased exercise tolerance and muscular strength, improvements in EKG, normalization of liver enzymes and increased mental acuity. According to his work, patients who had fatigue or low-level vitality who had taken 100 mg of a nucleic acid daily for one week felt much better.
As early as 1976 Dr. Frank discussed the benefits of dietary RNA nucleotides to boost the immune system and help reverse the effects of aging. His works described the use of RNA to boost the immune system, increase energy, improve skin elasticity, aid in memory, improve transplants and help protect the body from cancer. Subsequent work by Dr. Fusco and Dr. Rudolph support the early work of Frank. Working at the McGill Clinic, Dr. Cameron was able to demonstrate positive effects on memory following RNA supplementation. The brain has the highest concentration of RNA in the body so it is not surprising that dietary RNA has been found to have effects on memory and has also been suggested to affect neurotransmitter levels (Life Extension. January, 2003, Morgan P.J. Neuroendocrinology, 50, 1989).
RNA has also been used for over twenty-five years in another field of alternative healthcare, homeopathy. Natural RNA is available as a homeopathic drug. The method of making homeopathic dilutions is based on the theory that the homeopathic “remedy” becomes more potent as the material is increasingly diluted. The remedy is prepared by diluting and succussing the mixture (shaking it vigorously) until the point where there are no more actual molecules and what remains is simply the vibrational imprint. The vibrational essence of the particular medicine is imprinted on a carrier substance by succussion. It is as if the molecular imprint of the substance is left on the inert material.
The Homeopathic Pharmacopoeia of the United States includes a monograph for RNA and DNA. In 1971, the French physician Julian described the use of RNA and DNA as homeopathic drugs (O.A. Julian, Materia Medica of New Homeopathic Remedies, Beaconsfield Publishers Ltd., 1990). The HPUS states that RNA is effective for acrid dyspepsia, allergic (psoric) conditions, allergic reactions, arthralgia, bilary sycosis , cancerous conditions, chronic eczema, cortical and medullary hypoasthenia, dysthyroidism, enterneurosis, epilepsy, frigidity, herpes infection, hypotension, hypothyroidism, impotence, leucopoenia, lymphodema, mental over-exertion, muco-membranous entero-pancreatic syndrome, personality disorders in children, psychological and physical slowness, sexual hypoasthenia, slowness at school, tubercular conditions, vaginitis and varicose ulcers. Additionally, homeopathic compositions containing RNA have been used to treat viral infections (Masiello, U.S. Patent).
As is the case with food sources of RNA nucleotides, the homeopathic remedies described use unmodified RNA or DNA that are susceptible to the natural breakdown processes in the body. In comparison, the direction of RNA in conventional medicine has concentrated on developing modified, degradation resistant, patentable RNA molecules with elegant descriptions of proposed mechanisms of action. However, in alternative health care the focus has been on the beneficial effects of unmodified RNA and DNA nucleotides regardless of their potential degradation or mechanisms of activity. The very fact that RNA and DNA degrade rapidly may have led to an FDA status of GRAS for nucleotides and the general FDA policy concerning the recognized safety of natural nucleic acids.
While the basic RNA molecule with its four bases (A,C,G,U) is the same for dietary, nutritional, homeopathic and therapeutic purposes, studies have revealed that there are several ways in which the RNA carries out its function in cells. It is well known that these naturally occurring RNA based mechanisms are shared by mammals, plants and bacteria to regulate activities within their cells. Some of these modes of action have been well characterized and include actions that have been given the names of antisense technology and RNA interference mechanisms (Baulcombe, Science 297, 2002, Holzman, ASM News 68, 2002). In other cases, it is known that the RNA has a beneficial effect; however, the mechanism by which it operates is not known.
In spite of the fact that the mechanism by which dietary nucleotides and RNA work in the body is considered an open question, I did feel it was worth including the information from the prior book on RNA describing what is known about different modes of action of RNA in fields outside of food and dietary supports. I am not implying this is how these dietary nucleotides function, merely sharing this information for those who will not be satisfied by the vast amount of literature supporting the use of nucleotides/RNA. There are some that will continue to question the validity of using nucleotides/RNA in spite of the overwhelming evidence illustrating their value. So, I share what is known about the mode of action of RNA in other settings/systems to try to allay questions by those who need to know how and are not satisfied with documentation of activity. To be honest, I would probably be one of those who would need to know the how, if this was not a field I was so well versed in. So, I share the following for those who need some background on possibilities of how RNAs function for their own peace of mind.
The use of RNA technology in conventional medicine has been evolving for decades. The field of medicine includes the use of RNA as important medical diagnostic tools as well as the use of RNAs in clinical trials as potential drugs. Pharmaceutical companies and biotechnology companies are spending literally hundreds of millions of dollars to develop RNA and DNA based drug molecules to regulate RNAs in the body.
The recognized potential of RNA in medicine is validated by the increased focus on this field from a variety of areas within the scientific community. There are nearly thousands of new papers on RNA for medical indications published each year and billions of dollars has been spent worldwide by pharmaceutical companies trying to exploit the enormous potential of RNA. The National Institute of Environmental Health Sciences strongly states that research in RNA represents the most exciting development in biology of the decade and that RNA research should lead to cures for cancer, AIDS, heart disease, ALS (amyotrophic lateral sclerosis) and arthritis, among others.
Over a decade ago, the journal Science crowned RNAi as its“Breakthrough of the Year” in 2002 and Nobel laureate and RNAi pioneer Phillip Sharp, called it “the most exciting discovery in the last decade,” adding that “there’s not an area of biological science this will not touch.” The president, CEO, and director of Alnylam Pharmaceuticals, stated RNAi as “presenting perhaps the broadest new class of therapeutics since recombinant proteins and monoclonal antibodies” (Hood, E. Environ Health Perspect 112, 2004).
While the basic RNA molecule is the same for dietary, nutritional, homeopathic and therapeutic purposes, several mechanisms of action have been suggested to describe the way in which the RNA functions in cells. It is well known that several naturally occurring RNA based mechanisms are used by mammals, plants and bacteria to regulate cellular processes. RNAs can work as interfering RNA, antisense RNA, riboswitches and ribozymes. No one knows exactly how nutritional food sources of RNAs work but we do know that they are unmodified so that they will safely break down in the digestive tract.
We already know that natural RNA is seen by the body as a food and as such it is digested via the action of enzymes into the individual RNA bases, or back to the individual snap beads that we used to make our necklace. The consensus is that it has not been possible to use unmodified RNA in standard medical drug development because of its inherent tendency to degrade into its component building blocks. The direction of RNA research in conventional medicine has concentrated on developing modified degradation resistant, patentable RNA molecules with elegant descriptions of proposed mechanisms of action (Crooke, S., Antisense Drug Dev. 8, 1998) (Westphal, S. New Scientist, July, 2003). This would be analogous to permanently gluing the plastic snap beads of our necklace together so that they could not come apart. If we had managed to develop a new type of glue that we used for this purpose, then we might patent the glue and the process we use to glue our beads together. We would then be in a position to describe how the necklace affected our body if it never came apart, we were never able to take it off when we slept, showered or as we grew; we would then be in a position to describe its “mechanism of action.”
Using this approach, the type of RNA technology that has been most extensively investigated by pharmaceutical companies is called antisense technology. This technology was first described by Zamecnik and Stephenson in 1978 (Proc. Natl. Acad. Sci. 75, 1978). From the standard drug development standpoint, our body’s system to degrade natural RNAs is a disadvantage for pharmaceutical companies that want to use this approach (Cohen, CRC Press, 1989). As a result a variety of strategies have been employed to protect or modify the native forms of RNA and DNA for antisense technology to prevent the natural degradation processes in the body (Deshpande, Pharmaceutical News 3, 1996). This would be similar to using non biodegradable plastic containers that do not breakdown in the environment rather than more natural biodegradable products. While both of these products serve a role in society the plastics or other products that do not decay naturally are more likely to cause toxic or environmental problems in the future. Just as we have a wide variety of non biodegradable products that we can use daily, plastic containers, Styrofoam cups, aluminum cans to name a few, science has also been able to design a number of groups that when added to RNA or DNA will prevent their degradation in the body. A wide variety of chemical modifications to the RNA or DNA backbone have been found to stabilize the structure and prevent this natural decay in the body. The use of modified RNA or DNA, known as modified nucleotides is now widely recognized as a powerful tool for regulating the steps leading from RNA to protein (Dove, A. Nature 20, 2002).
While this field of medical drug development is known as “antisense” we need to bear in mind that antisense itself is actually a natural regulatory mechanism that the RNAs in our body utilize every day (Kramer, Nature, 421, 2003, Nemes Human Molecular Genetics, 9, 2000, Dolnick, Pharmacol. Ther, 75, 1997). The term “antisense technology” has come to be synonymous with the use of modified nucleotide backbones for drug development purposes. It is important to make the distinction between antisense as a natural mechanism by which RNA works and the modified nucleotide backbones that are used for drug development with this technology.
This ability of antisense technology to decrease the levels of mRNA has been capitalized on as an approach for the treatment of inflammatory conditions, antiviral agents, antibacterial agents and anticancer agents (Westphal S., July 19, 2003). As a result of the exquisite specificity that is possible with RNAs these modified antisense nucleotides are useful for specifically inhibiting unwanted gene expression in cells. The science in this field of antisense technology has progressed to the point where companies are designing specific RNAs targeted to regulate particular genes with a high degree of specificity.
These modifications to RNA or DNA to ameliorate natural nucleotide degradation create other types of problems. As a consequence, this field of nucleic acid technology continues to be hampered by the potential toxicity and costs associated with the current methodologies as well as the issues with efficient delivery methods. A general limitation on the therapeutic use of these modified nucleotides has been their poor ability to be absorbed by the body, better known as “poor bioavailablility”. Approaches to overcome this problem have resulted in the use of large quantities of these modified RNAs or DNAs for systemic purposes that are administered in such a way as to achieve high blood concentrations, i.e. though intravenous administration (Yu, Antisense Nucleic Acid Drug, Dec 13, 2003, Hogrefe, Antisense Nucleic Acid Drug, Dec 9, 1999). In addition, the use of these high concentrations of modified nucleotides has led to several instances of toxicity and failed clinical trials (Branch, A TIBS 23, 1998, Chemical & Engineering News, June 16, 2003) (Templin, l., Antisense Nucleic Acid Drug, Dec, 10, 2000, Black, Antisense Res., Dec 4, 1994).
Hundreds of millions of dollars have been spent so far in an attempt to utilize these modified RNAs or DNAs as a means of imitating a natural regulatory process (Chemical & Engineering News, April 28, 2003, Chemical & Engineering News, October 7, 2002, Chemical & Engineering News, May 6, 2002). Systemic delivery issues continue to plague this field. After almost ten years and nearly half a billion dollar pharmaceutical investment deal, a potential cancer drug that operates via an antisense mechanism remains stuck in clinical trials (Nature Biotechnology, September, 2004).
Despite their problems antisense RNAs and DNAs continue to sit at the forefront of molecular medicine as these modified nucleotide backbones progress through clinical trials. The expectation is that in the near future we will see approved, highly specific antisense drugs for systemic use. Albeit, these nucleotide based antisense drugs will have modified backbones, patented chemistries, high prices and precautionary notes on potential toxicity or adverse effects.
RNA interference (RNAi) in animals, plants and fungi is another natural regulatory mechanism that is used by plants and animals to protect themselves against invasion of foreign nucleic acids (Lau N. Scientific American August, 2003). This mechanistic pathway was first described by Andrew Fire and Craig Mello in 1998 (Nature, Feb, 1998) and has been reviewed and popularized by the writings of Gregg Hannon (Hannon, G. RNAi: A Guide to Gene Silencing, Cold Spring Harbor Press, 2003). Since that time it has been confirmed that this pathway is well conserved between plants and animals (Tisterman Science 295, 2002). Similar to antisense mechanisms RNAi regulates the activity of specific genes by binding to messenger RNA and preventing their translation into protein (Lagos-Quintana Science, 294, 2001). The regulation ultimately comes from the fact that no protein is made. In our construction model if someone were to cut all of our boards into pieces before we were able to build our sunroom it would be similar to RNA interference.
As is the case with antisense, the use of RNA interference has exploded as a potential tool for blocking expression of specific genes and is of huge therapeutic interest (Opalinska, Nature Reviews 50, 2002, Nature Reviews, Dec 2003). Rather than using modified nucleotides as in antisense technology, RNAi uses double stranded forms of the RNA to protect the RNA from breakdown. In order for RNAi to function it requires this double stranded RNA for stability from degradation. When single stranded interfering RNAs are used it requires almost 10 times the concentration of the double stranded versions. While interfering RNA is a useful laboratory tool, the utility of using interfering RNAs in vivo is severely hampered by the lack of efficient delivery systems (Frantz S. Nature Reviews Drug Discovery, Oct, 2003).
Interfering RNA technology is being widely used in the laboratory at this time and is still in the experimental stages for medicine. Recently an investigational new drug application has been filed for the use of siRNA. However, “Cy Stein, a pioneer in the antisense field, says siRNA molecules face the same delivery obstacles as other RNA-based drugs” (Nature Biotechnology, Sept, 2004).
Similar to the case of antisense technology, it is important to remember that RNAi is a naturally occurring regulatory mechanism that cells use everyday. Techniques are being designed to apply this natural technology for practical applications in the drug and diagnostic markets. Changes that are being made to its native structure are necessitated by the desire to protect the RNA from its inherent breakdown process so that it can be stable enough to be utilized for medical purposes. The field of interfering RNA continues to make almost daily strides in the application of this technology to unraveling pathways and molecular mechanisms in the body.
Ribozymes are yet another type of RNA mechanism of action that involves binding of RNA messages. The ribozyme acts to control this message by cutting it the way you would cut a string with a scissor. A difference between antisense mechanisms and ribozymes is that one ribozyme can turn off or cut multiple RNA messages. As with antisense or interfering RNA, it is important to keep in mind that this is a naturally occurring mechanism in cells. We can study it and describe it in isolation from its natural setting in order to understand it better. However, it is a mechanism used by your cells as part of a natural complement of regulatory pathways.
Inside a cell there are thousands of chemical reactions occurring on a daily basis in order for the cell to live, grow and respond to changes in its environment. These chemical reactions do not generally happen on their own – they are helped along by molecules called enzymes. For a long time it was believed that all enzymes were proteins. Nobel Prize laureates, Thomas Cech and Sidney Altman described the ability of RNA to act as an enzyme; this entity is given the name of ribozyme. This discovery helped to change the view of RNA as a passive carrier of information from DNA to protein to the perception of an active player in cellular activities. “A few years ago, before RNAi, siRNAs, microRNAs, and riboswitches, RNA was [seen as] the passive messenger that carried the information dutifully from the DNA to the protein-synthesizing machinery,” says Dr. Gerald Joyce. Now, he adds “there’s this whole secret society that’s really running quite a bit of the show within the cells” (Constans, A. The Scientist, May 24, 2004).
The use of ribozymes clinically has focused on anti viral agents. Work continues to progress using ribozymes to address HIV, herpes simplex virus as well as for cancer causing viruses. As with the case in antisense and interfering RNAs there are concerns over toxicity and delivery methodology. However, ribozymes have the potential to be unique, highly specific therapeutic tools.
Riboswitches are a newly discovered class of RNAs that regulate the amount of specific nutrients in a cell acting as molecular switches (Winkler, Nahvi, Collins, Breaker, Nature, March 18, 2004). These riboswitches are a type of ribozyme in that they are able to cleave or cut the RNA message. What makes riboswitches unique is that the nutrient they regulate can actually bind to the riboswitch. This is quite logical if you think about it. If your body is making too much vitamin B1, the extra B1 in your cells will bind to a specific riboswitch. The riboswitch then “tells” your body to stop making so much B1. This occurs when excess B1 binds to the riboswitch, which responds by cutting your RNA information molecule for B1 like a scissor cutting a piece of ribbon. The riboswitch acts like a switch that can either turn the manufacture of nutrients in a cell on or off depending on the body’s demand for them. It is a control mechanism for your body’s production lines for individual nutrients. The riboswitch “talks to your cells” the way a foreman at a production plant might talk to the workers on the production line to let them know that production was exceeding demand. This riboswitch is actually a part of the very same RNA message that contains the information to make the nutrient.
When an excess of this nutrient is detected in the cells, it can attach to the portion of the information molecule, the RNA. This RNA with the bound nutrient now has a different shape and it can cut the message so that production stops. The mRNA for a particular nutrient actually contains a riboswitch RNA segment that is directly involved in controlling its own activity. “Not only is this a new class of ribozyme but it also is the first example of a ribozyme that directly senses a metabolite for the purpose of genetic control” says Breaker, whose lab first described this unique class of RNAs. Riboswitch RNAs have been identified in cells that control the synthesis of a variety of well known vitamins and nutrients, including B1, B2, and B12, nucleotide bases as well as the control of s adenosyl methionine, otherwise known as SAMe. Riboswitches are able to both turn off genes as well as to turn on genes, as is the case with the amino acid glycine (Mandal, M. Science, Oct 8, 2004).
Just as we have seen with antisense and interfering RNA, riboswitches are naturally occurring regulatory mechanisms that your cells use on a regular basis. Because this control mechanism depends only on the RNA and the environment, it is particularly intriguing. “It’s a completely new, unsuspected way of controlling gene expression” says David Lilley, professor of molecular biology, University of Dundee, Scotland. According to Ron Breaker whose lab at Yale first described these molecules, “Riboswitches are like a little chunk of the lost RNA world” (Travis, J., Science News, April, 2004).
Many scientists believe that before the emergence of the first cell, RNA was the dominant, and probably the only, form of life. The idea is that life existed using only RNA and that proteins came later. The term “RNA World” was first coined by Nobel Prize laureate Walter Gilbert to describe this hypothesis. The discovery of riboswitches that use only RNA and the environment for their regulation lends support to this hypothesis.
Gerald Joyce, member of the National Academy of Science, studies this RNA evolutionary process in his laboratory at Scripps Research Institute. “Our studies of RNA-based evolution are relevant to understanding the early history of life on Earth. It is believed that an RNA-based genetic system (the “RNA world”) preceded the DNA and protein-based genetic system that has existed for 3.5 billion years. Our research aims to recapitulate the biochemistry of the RNA world in the laboratory. We use in vitro evolution to explore the catalytic potential of RNA, especially to search for RNA enzymes that have the ability to catalyze their own replication” (Gerald Joyce).
“The modern switches that we see in cells today might be directly descended from RNAs that were present some three or four billion years ago in the RNA world,” says Breaker. “Further probes into structured RNAs may reveal that the road does not end at riboswitches.”
“Each time we learn something more”, says Ellington, “it seems as though there’s an even greater network of complexity that we didn’t appreciate previously. I’m not sure where it will stop” (Constans, A. The Scientist, May 24, 2004).
This thought is echoed by Nobel Prize laureate Thomas Cech, “Is there no end to the versatility of RNA?” (Cech, T. Nature, March 18, 2004).
RNA can act to help regulate a cells activity, via these well defined modes of activity in the body including antisense, RNA interference, riboswitches, ribozymes, small interfering RNAs, micro RNAs and most likely many more to be discovered at some point in the not too distant future. Please recognize that all of these mechanisms are naturally occurring ways in which RNA can and does function in cells; your cells, plant cells, yeast cells and animal cells – naturally occurring mechanisms.
Conservatively speaking, your cells may contain 100,000 different RNAs at any one time. Some of these natural RNAs that are always a part of your cells may be working via any or all of these mechanisms at any one time. Scientists have been able to discover and describe the individual ways in which RNAs can behave precisely because of the fact that these modes of action occur naturally and simultaneously in cells. The individual processes, such as interfering RNA, can then be isolated and teased out from the total mixture in order to study and describe them in more detail.
RNA has been shown to function in a variety of regulatory capacities. Research from Yale has demonstrated RNAs that function as “riboswitches” do not require protein factors for function (Nature, March 18, 2004). These riboswitches are used to sense compounds that are fundamental to all living systems. Riboswitches are dual function molecules that undergo conformational changes and communicate metabolite binding. In addition to riboswitches, the past decade has seen the discovery of naturally occurring interfering RNAs and short interfering RNAs. Prior to that time regulatory roles have been described for ribozymes, antisense RNA, decoy RNA, aptamers, immunostimulatory CpG motifs and RNA‑dependent‑DNA methyltransferases as a means to regulate DNA methylation.
The Yale researcher Ron Breaker, whose lab discovered riboswitches has suggested that we may not yet be finished uncovering new types of RNA or novel mechanisms or action for RNA, “It makes you wonder how many other chunks of the RNA world are not entirely lost” (Science News, April, 2004).
Even regions of the DNA that are not made into recognizable protein are still converted into their respective RNA counterparts. Recently some of this “extra” RNA was found to act by regulating and affecting the gene next to it, in other words, it regulates its next door neighbor. Non-coding RNAs and so called non functional RNAs have often been dismissed as “noise” (Schmit, S. Nature, June, 2004). However, on closer inspection there is an accumulating amount of literature to suggest that we have only just begun to explore the possible uses and functions of these RNA.
MicroRNAs or miRNAs have been found in all animals and plants and they are now known to be one of the most abundant non coding RNAs to regulate the activity of genes, and their expression is highly tissue specific (Clarkson, S. Nature Reviews Microbiology, June, 2004).
Stem cells are universal cell types with the possibility of becoming any cell. Minuscule RNA molecules have now been discovered that act on these stem cells to guide them to develop into specific cells with defined functions (Couzin, J. Science Now, March, 2004). And yes, it does appear that we are getting smaller and smaller with the RNAs, as we go from small interfering to micro to minuscule. It is hard to imagine what will be next, but that is precisely the point!
RNAs have been found to have a direct role in both mating and fertility. RNA triggers the switch between sexes or mating types in yeast (Pilcher, H. Nature, April, 2004.). In human fertilization, it has been discovered that the fathers RNA is delivered to the egg. These male RNAs had been disregarded as “leftovers” from normal sperm production. However, now it appears that these paternal RNAs may serve a role in early development (Ostermeier, G. Nature, May, 2004). Additional RNAs have been described to be involved in egg development (Science, Nov, 2003). Noncoding RNAs are also involved in germ cell formation; germ cells are the cells of either sex that are involved in the creation of a new organism (Martinho, RG et al, Curr. Biol. 14, 2004).
Cells in the body are generally not found in isolation; rather they tend to communicate with other cells or non-cellular components of their environment. Recently RNAs have also been found to be directly involved in cell spreading, which is part of the attachment and signaling that occurs in this type of physical cell to cell communication (de Hoog, CL., Cell, May, 2004).
RNAs have also been implicated in the formation of inorganic or non-living materials. A group from the chemistry department at North Carolina State University has been able to use RNA to induce the formation of hexagonal crystals (six sided) from the metal palladium (Chemical Eng News, April, 2004). Gerald Joyce, a recognized expert in RNA, who has been able to spontaneously fold a piece of DNA into an octahedron (an eight sided figure) in his own lab at the Scripps Research Institute, has a classic understatement on the growth of these palladium crystals “RNA is very good at positioning metals” (Science News, April, 2004). These findings raise some interesting questions, “Is RNA in the environment actively evolving inorganic materials? Was RNA important in establishing an inorganic component of the RNA world, an inorganic component that may have facilitated a variety of unforeseen RNA activities?” (Gugliotti, L. Science, May, 2004).
The discovery of all of these new RNAs serves to emphasize the fact that the field of RNA is in its infancy. What we know or think we know today about RNA will quickly be replaced and expanded upon in the future.
In terms of how unmodified RNAs and nucleotides work, the answer may be via every naturally occurring regulatory system that is utilized by RNA in the cells, or by none of these mechanisms. RNAs may have the capability to function via any naturally occurring regulatory system in a cell which would include RNA interference, antisense, riboswitches, ribozymes, small interfering RNA, micro RNA and any other mechanisms to be defined in the future that work by utilizing RNA.
We do not know what other regulatory roles will be ascribed to RNA and nucleotides in the future. Clearly, RNA and nucleotides serve a multifaceted role as a regulatory molecule in cells. It is important to remember that these described mechanisms are naturally occurring processes that cells use for self-regulation and maintenance. It is possible that RNA nucleotides may operate by some, all, or none of these naturally occurring mechanisms serving as nutrient sensors to help balance activities within the cell.