Topic of the Month

RNA interference
By Suzanne Kadereit

Upfront a word of warmest thanks to the Nature Publishing Group (www.nature.com), Developmental Cell (www.developmentalcell.com/) and Science (www.Sciencemag.org) for graciously providing us with full text access to some of the listed papers.

In recent years, RNA interference (RNAi) has been probably one of the fastest-developing areas in science, and it has gone from nothing to a full-fledged field in only five years. The short list of papers presented here is intended to provide a brief overview of this fascinating field.

RNAi hit the headlines in 1998 when Fire et al. reported potent and specific interference with gene expression after injecting double-stranded RNA (dsRNA) into C. elegans. Moreover, the effect could be propagated to the F1 progeny. Most surprising, however, was the finding that only a few molecules of dsRNA could interfere with the expression of abundant mRNAs, strongly suggesting the involvement of a catalytic step.

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. ABSTRACT
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998). Nature 391:806.

A slew of papers successfully using RNAi to identify gene function followed, culminating in reports of large-scale analyses, such as:

Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions. FULL TEXT
Simmer F, Moorman C, Van Der Linden AM, Kuijk E, Van Den Berghe PV, Kamath R, Fraser AG, Ahringer J, Plasterk RH (2003). PLoS Biol 1:E12.

And in case you have been wondering all along how RNAi spreads so elegantly from cell to cell:

Transport of dsRNA into cells by the transmembrane protein SID-1. ABSTRACT
Feinberg EH, Hunter CP (2003). Science. 2003 301:1545.

Not surprisingly, there has been great excitement about the potential for clinical applications of RNAi. However, in light of this, a question that was overlooked before, became very pertinent. The effects of double-stranded RNA (dsRNA) on activation of the interferon system, as well as its direct impact on translational control, have been studied for decades and documented extensively.

Despite this, relationship between RNAi and known dsRNA-activated cellular pathways was only investigated recently. The resulting studies showed that the RNA interference machinery functions independently of the interferon system. However, siRNAs do activate the interferon system and result in upregulation of interferon-induced genes, and this could place severe limitations on the potential for clinical applications of RNAi.

Activation of the interferon system by short-interfering RNAs. FULL TEXT
Sledz CA, Holko M, de Veer MJ, Silverman RH, Williams BR (2003). Nat Cell Biol 5:834.

Induction of an interferon response by RNAi vectors in mammalian cells. FULL TEXT
Bridge AJ, Pebernard S, Ducraux A, Nicoulaz AL, Iggo R (2003). Nat Genet 34:263.

As many scientists enthusiastically adopted RNAi technology as a research tool to knock-down genes of interest, others investigated the mechanism underlying this intriguing "new" phenomenon. For a review about the machinery behind RNAi:

RNA interference. ABSTRACT
Hannon GJ (2002). Nature 418:244.

It is also now apparent, that RNAi is part of a bigger picture of non-coding RNA (ncRNA) biology. Now we have snRNAs, snoRNAs, siRNAs, miRNAs, shRNAs, rasiRNAs and other small ncRNAs. These ncRNAs have a variety of functions, including editing of mRNA transcripts, post-transcriptional control, chromatin stability, chromosome cohesion, histone methylation, imprinting, even roles in diseases.

Sean Eddy's review gives a historical overview of the world of these non-coding RNAs, puts context around the phenomenon of RNA interference and depicts a fascinating modern world of RNA biology.

Non-coding RNA genes and the modern RNA world. FULL TEXT
Eddy SR (2001). Nat Rev Genet 2:919.

And a comprehensive, and most recent, overview of the field of small RNAs and a nice figure depicting the historical time line of discovery, are given in:

microRNAs: Runts of the Genome Assert Themselves. ABSTRACT
Lai EC (2003). Curr Biol 13:R925.

Recent work demonstrated that there are specific expression profiles for ncRNAs, depending on the cell type and developmental stage, and that the RNAi machinery fulfills crucial cellular functions very early in development, as its impairment results in severe phenotypes.

The small RNA profile during Drosophila melanogaster development. ABSTRACT
Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
Gaasterland T, Meyer J, Tuschl T (2003). Dev Cell 5:337.

Embryonic stem cell-specific MicroRNAs. ABSTRACT
Houbaviy HB, Murray MF, Sharp PA (2003). Dev Cell 5:351.

Dicer is essential for mouse development. ABSTRACT
Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, Li MZ, Mills AA, Elledge SJ, Anderson KV, Hannon GJ (2003). Nat Genet 35:215.

The microRNA-producing enzyme Dicer1 is essential for zebrafish development. ABSTRACT
Wienholds E, Koudijs MJ, van Eeden FJ, Cuppen E, Plasterk RH (2003). Nat Genet 35:217.

And to finish, perhaps one of the most fascinating newly-emerging roles of the RNAi machinery: a role in the epigenetic control of chromatin. The following review and papers give an overview on epigenetic control of gene expression and a basis for recent advances in the understanding of heterochromatin (silent chromatin) regulation, by RNAi and small ncRNAs, transcribed from repetitive sequences and transposons dispersed throughout the genome.

Heterochromatin and epigenetic control of gene expression. FULL TEXT
Grewal SI, Moazed D (2003). Science 301:798.

Establishment and maintenance of a heterochromatin domain. ABSTRACT
Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI (2003). Science 297:2232.

Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. ABSTRACT
Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002). Science 297:1833.

Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. ABSTRACT
Schramke V, Allshire R (2003). Science 301:1069.

It remains to be seen whether the usage of siRNAs as tools to inhibit gene expression has also the added effect of chromatin modifications at the loci of the targeted genes.

Additional reading can be found at the RNAi web focus by NPG at http://www.nature.com/focus/rnai/.

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Updated: April 12, 2004