RNAi is a gene-silencing phenomenon triggered by double-stranded (ds) RNA and involves the generation of 21 to 26 nt RNA segments that guide mRNA destruction. In Caenorhabditis elegans, lin-4 and let-7 encode small temporal RNAs (stRNAs) of 22 nt that regulate stage-specific development. Here we show that inactivation of genes related to RNAi pathway genes, a homolog of Drosophila Dicer (dcr-1), and two homologs of rde-1 (alg-1 and alg-2), cause heterochronic phenotypes similar to lin-4 and let-7 mutations. Further we show that dcr-1, alg-1, and alg-2 are necessary for the maturation and activity of the lin-4 and let-7 stRNAs. Our findings suggest that a common processing machinery generates guide RNAs that mediate both RNAi and endogenous gene regulation.

We have investigated the role of trigger RNA amplification during RNA interference (RNAi) in Caenorhabditis elegans. Analysis of small interfering RNAs (siRNAs) produced during RNAi in C. elegans revealed a substantial fraction that cannot derive directly from input dsRNA. Instead, a population of siRNAs (termed secondary siRNAs) appeared to derive from the action of a cellular RNA-directed RNA polymerase (RdRP) on mRNAs that are being targeted by the RNAi mechanism. The distribution of secondary siRNAs exhibited a distinct polarity (5'-->3' on the antisense strand), suggesting a cyclic amplification process in which RdRP is primed by existing siRNAs. This amplification mechanism substantially augments the potency of RNAi-based surveillance, while ensuring that the RNAi machinery will focus on expressed mRNAs.

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RNA interference (RNAi) is a broadly used reverse genetics method in C. elegans. Unfortunately, RNAi does not inhibit all genes. We show that loss of function of a putative RNA-directed RNA polymerase (RdRP) of C. elegans, RRF-3, results in a substantial enhancement of sensitivity to RNAi in diverse tissues. This is particularly striking in the nervous system; neurons that are generally refractory to RNAi in a wild-type genetic background can respond effectively to interference in an rrf-3 mutant background. These data provide the first indication of physiological negative modulation of the RNAi response and implicate an RdRP-related factor in this effect. The rrf-3 strain can be useful to study genes that, in wild-type, do not show a phenotype after RNAi, and it is probably the strain of choice for genome-wide RNAi screens.

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Previous studies indicated that the vaccinia virus D10 protein, which is conserved in all sequenced poxviruses, participates in the rapid turnover of host and viral mRNAs. D10 contains a motif present in the family of Nudix/MutT enzymes, a subset of which has been shown to enhance mRNA turnover in eukaryotic cells through cleavage of the 5 cap (m 7 GpppNm-). Here, we demonstrate that a purified recombinant D10 fusion protein possesses an intrinsic activity that liberates m 7 GDP from capped RNA substrates. Furthermore, point mutations in the Nudix/MutT motif abolished decapping activity. D10 has a strong affinity for capped RNA substrates (K m Ϸ 3 nm). RNAs of 24 -309 nt were decapped to comparable extents, whereas the cap of a 12-nt RNA was uncleaved. At large molar ratios relative to capped RNA substrate, competitor m 7 GpppG, m 7 GTP, or m 7 GDP inhibited decapping, whereas even higher concentrations of unmethylated analogs did not. High concentrations of uncapped RNA were also inhibitory, suggesting that D10 recognizes its substrate through interaction with both cap and RNA moieties. Thus far, poxviruses represent the only virus family shown to encode a Nudix hydrolase-decapping enzyme. Although it may seem self-destructive for a virus to encode a decapping and a capping enzyme, accelerated mRNA turnover helps eliminate competing host mRNAs and allows stagespecific synthesis of viral proteins.mRNA metabolism ͉ MutT motif ͉ Nudix hydrolase ͉ poxvirus ͉ mRNA turnover T he steady-state concentration of an mRNA is determined by synthesis and decay, allowing cells to rapidly adapt their pattern of gene expression (1). Similarly, some viruses accelerate mRNA turnover to suppress synthesis of cellular proteins and regulate expression of their own genes (2). Studies of vaccinia virus (VACV), the laboratory prototype poxvirus, indicated that viral mRNAs are relatively unstable compared with those of uninfected cells (3, 4). Thus, rapid mRNA turnover coupled with robust and sequential transcription of viral early, intermediate, and late genes allow stage-specific protein synthesis (5). Likewise, VACV infection induces the destabilization of cellular transcripts, a process thought to contribute to the shutdown of host protein synthesis (6-9). The latter may enhance viral replication by alleviating competition from cellular mRNAs for the protein synthetic machinery and by diminishing host antiviral responses. Nevertheless, the mechanisms used by VACV to regulate mRNA turnover have not been elucidated.The VACV D9 and D10 proteins were identified as putative negative regulators of gene expression during a transfectionbased DNA library screen used to isolate activators of late VACV transcription (10, 11). Both proteins are highly conserved: D10 homologs are present in all sequenced poxviruses, and D9 homologs are in all members of the chordopoxvirus subfamily. Overexpression of D10 during infection significantly reduced the amount of VACV transcripts, and overexpression of D9 had a similar but lesser effect (11). Remarkabl...

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students.

Vaccinia virus (VACV) encodes enzymes that cap the 5 end of viral mRNAs, which enhances their stability and translation. Nevertheless, recent studies demonstrated that the VACV D10 protein (VACV-WR_115) decaps mRNA, an enzymatic activity not previously shown to be encoded by a virus. The decapping activity of D10 is dependent on a Nudix hydrolase motif that is also present in the VACV D9 protein (VACV-WR_114), which shares 25% sequence identity with D10. Here, we showed that a purified recombinant VACV D9 fusion protein also decaps mRNA and that this activity was abolished by point mutations in the Nudix hydrolase motif. Decapping was specific for a methylated cap attached to RNA and resulted in the liberation of m 7 GDP. D9 differed from D10 in requiring a longer capped RNA substrate for optimal activity, having greater sensitivity to inhibition by uncapped RNA, and having lower sensitivity to inhibition by nucleotide cap analogs unattached to RNA. Since D9 is expressed early in infection and D10 late, we suggest that the two proteins enhance mRNA turnover and manipulate gene expression in a complementary and overlapping manner.The regulation of mRNA turnover allows a cell to rapidly adjust gene expression in an adaptive manner. Vaccinia virus (VACV), the prototype for the laboratory study of poxviruses, modulates both viral and host gene expression during the course of infection (12). The double-stranded DNA genome of VACV encodes approximately 200 proteins that are expressed in sequential stages delineated as early, intermediate, and late (13, 16). Although a transcriptional cascade drives entry into each phase of gene expression, rapid turnover eliminates viral mRNAs soon after their synthesis ceases, thereby augmenting progression through the virus life cycle (1). VACV infection also triggers the degradation of cellular mRNAs (2, 5), which contributes to the shutdown of host protein synthesis.A clue to the mechanism of accelerated cellular and viral mRNA degradation was obtained during studies designed to identify positive transcriptional regulators. Shors and coworkers (18) reported that overexpression of gene VACV-WR_115 (D10R) and to a lesser extent VACV-WR_114 (D9R) decreased expression of viral proteins and the quantity of transcripts possessing a 5Ј cap, a structural feature of both cellular and viral messages. In contrast, a mutant virus with a deletion of the D10R gene displays persistence of cellular and viral transcripts, a delay in shutoff of host protein synthesis, and replication defects (14). Taken together, these data suggested that the D10 protein (the product of the D10R gene) regulates mRNA stability and consequently the amount and duration of host and viral proteins synthesized. Although a D9R deletion mutant virus did not exhibit replication defects in tissue culture cells, a mutant virus with deletions of both the D9R and D10R genes could not be isolated, suggesting that these two proteins have compensating functions (14). Moreover, the individual importance of D9 and D10 is reflected i...