Interesting article

[Meem]

By Jef Akst
Translation Revelation
More findings confirm that small RNAs work in mysterious ways.


Fluorescent FT protein in the phloem of an Arabidopsis plant.
© Jean-Francois Podevin / Photo Researchers, Inc.
Nearly 20 years after its discovery, RNA interference (RNAi) is part of biology’s orthodoxy. Small RNA molecules can disrupt gene expression by degrading messenger RNAs (mRNAs) on their way to becoming proteins, or otherwise interfering with translation. But the discovery that these same small RNA molecules might be able to do just the opposite—enhance gene expression—was somewhat heretical.

In 2007, molecular biologist Shobha Vasudevan of Yale University and her colleagues produced the unanticipated findings: Small RNA molecules known to be involved in RNAi, known as microRNAs (miRNAs), can activate translation, promoting the conversion of mRNAs to proteins. It was a “surprise finding,” Vasudevan recalls.

Further investigation revealed that activation occurred only during cell-cycle arrest, induced by serum starvation. In actively growing cells, on the other hand, miRNAs suppressed translation. The exact mechanism of activation is unclear, Vasudevan says, but it appears to involve the recruitment of Argonaute (AGO) proteins—known participants in the RNAi pathway—and fragile X mental retardation–related protein 1 (FXR1). These proteins combine with the miRNA to form complexes that bind to the 3' untranslated region (3'-UTR) of the mRNA of tumor necrosis factor-α (TNFα) to initiate translation.

This discovery was hot on the heels of another unexpected finding—that of RNA activation (RNAa) at the level of gene transcription. Just one year earlier, molecular biologists Long-Cheng Li and Robert Place and their colleagues at the University of California, San Francisco, found that small RNAs could switch on gene transcription1—a finding that was corroborated just a few months later by a group of researchers working independently at the University of Texas Southwestern Medical Center at Dallas.2 (See the May 2009 issue of The Scientist.) And last year, additional research revealed more of the mysterious qualities behind translation activation by miRNA.

“These papers are making us look at miRNAs as a far more versatile system of regulating gene expression,” says Vasudevan, now at Massachusetts General Hospital and Harvard Medical School.

The wrong end
Five months after the publication of this month’s hot paper, Anders Lund of the University of Copenhagen in Denmark and his colleagues discovered another example of miRNA-mediated translation activation—this time of mRNAs that encode ribosomal protein.3 “We were looking for just general targets for miR-10a”—an miRNA broadly expressed in mice, Lund recalls. “What we found, which was very much a surprise,” was that miR-10a interacts with several ribosomal protein mRNAs to stimulate their translation. Even more bizarre, however, was the target: miR-10a appeared to be acting on the 5'UTR of ribosomal mRNA—the so-called 5'-terminal oligopyrimidine tracts, or 5'TOP motif. miRNAs predominately suppress gene expression by binding to target sites in the 3'UTR of mRNAs—the end of the mRNA strand where translation is completed.

It doesn’t make sense, Lund says. Placing an miRNA complex in between the 5' mRNA cap—which normally recruits the small ribosome to initiate translation—and the AUG start codon seems “obstructive,” Lund says, “unless [there is] some completely different mechanism.”

Later in 2008, yet another example of miRNA translation activation emerged. In a study led by virologist Michael Niepmann of Justus-Liebig-University Giessen in Germany, the researchers discovered that the liver-specific miR-122 could stimulate translation of hepatitis C virus (HCV) mRNAs. In this case, miR-122 interacted with two target sites to enhance the association of the viral RNA with the host ribosomes.4 The targets were, again, at the 5' end of the mRNA. Most recently, this October, researchers published a third report of 5'UTR translation activation, in which miR-346 targets the 5'UTR of receptor-interacting protein 140 (RIP140), a transcriptional corepressor.5

Whether targeting the 5'UTR is a common mechanism of miRNA translation activation, “it’s way too early to say,” Lund says. Indeed, this past summer, biochemist Yukihide Tomari of the University of Tokyo and his colleagues showed that miRNAs targeting the 3'UTR activated translation under certain conditions—specifically, when the target mRNA lacks a poly(A) tail, present at the 3' end. “We are (almost hopelessly) puzzled as to mechanistically how such translational activation can occur,” Tomari says in an email.

“I think it is clear that there’s no universal mechanism,” says RNAi researcher Timothy Nilsen of Case Western Reserve University in Ohio, “and it’s going to be important to find out in what context you can either up-regulate or down-regulate [gene expression].”

In the clinic
The discovery that miRNAs can enhance gene expression has captured the attention of the biotechnology sector. Place, for one, has sold his technology regarding miRNA activation of transcription to Massachusetts-based Alnylam Pharmaceuticals for therapeutic development, and is currently looking to license the technology for reagent development to a company that he declined to name.

In September of this year, molecular biologist Seppo Ylä-Herttuala of the University of Kuopio in Finland and Ark Therapeutics, along with his colleagues, published the first demonstration that small RNAs can be delivered by a lentriviral vector to up-regulate transcription in vivo.6 “I’m pretty sure that this is a general mechanism that is used for fine-tuning gene expression at the nuclear level,” Ylä-Herttuala says, meaning that it could have broad applications for developing reagents as well as (eventually) therapeutic treatments.

Place sees just as much potential for the up-regulation of translation, which evades epigenetics by targeting mRNAs in the cytoplasm. “We don’t know [yet] to what extent we can exploit translation activation,” Place says, “[but] if it can be [broadly applied] to any given transcript, that technology is essentially limitless.”

Data derived from the Science Watch/Hot Papers database and the Web of Science (Thomson ISI) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age.
S. Vasudevan, et al., “Switching from Repression to Activation: MicroRNAs Can Up-regulate Translation,” Science, 318:1931–34, 2007. (Cited in 250 papers)
References
1. L.C. Li et al., “Small dsRNAs induce transcriptional activation in human cells,” Proc Natl Acad Sci, 103:17337–42, 2006.
2. B.A. Janowski et al., “Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs,” Nat Chem Biol, 1:216–22, 2005.
3. U.A. ￘rom et al., “MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation,” Mol Cell, 30:460–71, 2008.
4. J.I. Henke et al., “microRNA-122 stimulates translation of hepatitis C virus RNA,” EMBO J, 27:3300–10, 2008.
5. N.-P. Tsai et al., “MicroRNA mir-346 targets the 5'UTR of RIP140 mRNA and up-regulates its protein expression,” Biochem J, 423:TK, 2009.
6. M.P. Turunen et al., “Efficient regulation of VEGF expression by promoter-targeted lentiviral shRNAs based on epigenetic mechanism,” Circ Res, 105:604–9, 2009.


Advertisement



****

Rate this article
Currently 3.42/512345
Rating: 3.42/5 (33 votes )


Comment on this article


Return to Top
comment:
RNAs Mysterious Ways
by Dov Henis

[Comment posted 2009-12-24 14:55:15]
RNAs Mysterious Ways


Translation Revelation
More findings confirm that small RNAs work in mysterious ways.
LINK


I suggest that unraveling the mysterious ways of RNAs would plainly follow:

- 1st, acceptance of the revelation of the commonsensical lifehood of genes, of the concept presented in "Updated Life's Manifest May 2009"
LINK

- 2nd, a rational resolution of the question if/when the initial, independent pre-biometabolism sunlight-fueled genes were RNAs and if/when they evolved into DNAs prior to celling and genoming, and

- 3rd, a resolution of the rational possibility that ALL RNAs are representative of the original archae-genes rendered into the primary nessengers-toolings of their DNA genes-genomes follow-ups, and

- 4th, acceptance of the rational possibility that the RNAs are also the environmental feed-back communicators to the genomes thus signallers of accordingly biased genes expressions effectors,

- 5th, effecting the genes expressions per "Genes' Expression Modification"
LINK


Suggesting,

Dov Henis
(Comments From The 22nd Century)


Return to Top
comment:
It's just RNAi against regulatory non-coding RNAs
by kevin morris

[Comment posted 2009-12-24 12:19:18]
Just out of curiousity doesn?t anybody read the literature anymore? If one were to look some of the key observations as to the mechanism for siRNA mediated gene activtion has already been worked out [1-3] and reviewed in [4]. As for miRNAs they don?t just target mRNAs but also antisense non-protein-coding RNAs that have transcriptional regulatory functions (See supplemental data in [1]).


Literature cited:
1. Morris, K.V., et al., Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet, 2008. 4(11): p. e1000258.
2. Schwartz, J.C., et al., Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol, 2008.
3. Yu, W., et al., Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature, 2008. 451(7175): p. 202-6.
4. Morris, K.V., RNA-Directed Transcriptional Gene Silencing and Activation in Human Cells. Oligonucleotides, 2009.

[Meem]

This article reminds me of something a fellow mentioned to me on another website. He runs a research lab and was dumbfounded by something. He said, "I've added something to mitochondria which makes them turn into spheres. I have absolutely no idea why, or what it means."

[labelwench]

Perhaps this bit from Wikipedia will be helpful for people reading the article.

From Wikipedia, the free encyclopedia

In genetics, microRNAs (miRNAs) are single-stranded RNA molecules of 21-24 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (i.e. they are non-coding RNAs); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA. Mature miRNA molecules are either fully or partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression. The first miRNA was described in 1993 by Lee and colleagues in the Victor Ambros lab[1], but the term microRNA was only introduced in 2001 when the abundance of these tiny regulatory RNAs was discovered and reported in a set of three articles.[2][3][4] It is now known that miRNAs regulate the expression of more than half of all human protein-coding genes, and that the proper functioning of certain miRNAs is important for preventing cancer and other diseases.[5]

More regarding the relationship to disease:

miRNA and disease

Just as miRNA is involved in the normal functioning of eukaryotic cells, so has dysregulation of miRNA been associated with disease. Disease association in turn has led to increased funding opportunities for academic research and financial incentives for development and commercialization of miRNA-based diagnostics and therapeutics. After early commercialization aimed at academic research support was established, the initial research focus based on products and services requested was on cancer and neuroscience research. During 2007, interests indicated by product and services requested broadened to include cardiac research, virology, cell biology in general and plant biology.[33] A manually curated database miR2Disease that aims at documenting known relationships between miRNA dysregulation and human disease is publicly available. [47]