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Translation Revelation

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

By | December 1, 2009

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)

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. ├śrom 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.

Comments

Avatar of: anonymous poster

anonymous poster

Posts: 1

December 23, 2009

Actually, it's been just over 10 years since the discovery of RNAi ("nearly 20" is a bit of a stretch):\n\nPotent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.\nFire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Nature. 1998 Feb 19;391(6669):744-5.
Avatar of: anonymous poster

anonymous poster

Posts: 1

December 23, 2009

Unfortunately, the article focuses mostly on miRNAs and research that has been out for a year or two (its a rapidly evolving field)! \n\nIn terms of the 5'UTR binding, Darnell's group recent paper with Ago-CLIP indicates that only 1% of Ago-miRNAs are bound to 5'UTRs (40% on 3'UTRs) in whole brain extracts (Chi SW et al, 2009), therefore as far as miRNA-Ago complexes are concerned they don't show preference for 5'UTRs. Data from other groups also supports this. The examples described are most likely context specific exceptions (for miRNAs).\n\nHowever, apart from miRNAs there is a significant amount of literature on novel small and/or long RNAs identified through new generation sequencing. miRNAs are just the tip of the iceberg in an emerging RNA world!
Avatar of: Vinod Nikhra

Vinod Nikhra

Posts: 48

December 24, 2009

Long after the discovery that small RNA molecules can disrupt gene expression by degrading mRNAs, the finding by Shobha Vasudevan et al that Small RNA molecules can actually activate translation too, promoting the conversion of mRNAs to proteins, should not add to any confusion. This appears to be just the dual control prevalent in the biological systems.\n\nVinod Nikhra, MD\nwww.vinodnikhra.com
Avatar of: kevin morris

kevin morris

Posts: 1

December 24, 2009

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]). \n\n\nLiterature cited:\n1. Morris, K.V., et al., Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet, 2008. 4(11): p. e1000258.\n2. Schwartz, J.C., et al., Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol, 2008.\n3. Yu, W., et al., Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature, 2008. 451(7175): p. 202-6.\n4. Morris, K.V., RNA-Directed Transcriptional Gene Silencing and Activation in Human Cells. Oligonucleotides, 2009.\n\n\n
Avatar of: Dov Henis

Dov Henis

Posts: 97

December 24, 2009

RNAs Mysterious Ways\n\n\nTranslation Revelation\nMore findings confirm that small RNAs work in mysterious ways.\nhttp://www.the-scientist.com/article/display/56173/\n\n\nI suggest that unraveling the mysterious ways of RNAs would plainly follow:\n\n- 1st, acceptance of the revelation of the commonsensical lifehood of genes, of the concept presented in "Updated Life's Manifest May 2009"\nhttp://www.the-scientist.com/community/posts/list/140/122.page#2321\n\n- 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\n\n- 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\n\n- 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,\n\n- 5th, effecting the genes expressions per "Genes' Expression Modification" \nhttp://www.the-scientist.com/community/posts/list/200/122.page#3649\n\n\nSuggesting,\n\nDov Henis\n(Comments From The 22nd Century)
Avatar of: ROULETTE Wm. SMITH

ROULETTE Wm. SMITH

Posts: 10

January 8, 2010

With the many "surprising" and "mysterious" findings and "ways," are there any investigators or research teams exploring transmissible and infectious consequences of selected "small RNAs" when they are out of context? Insofar as selected viral small RNAs may contribute to a myriad of syndromes and diseases via a process dubbed 'autovirulence' (Smith RW, AIDS and 'Slow Viruses', Annals NYAS 1984, 437:576-607), why not pursue fault and error analyses of traditional small RNAs?

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