Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes

Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance

Posttranscriptional gene silencing (PTGS) in plants resuits from the degradation of mRNAs and shows phenomenological similarities with quelling in fungi and RNAi in animals. Here, we report the isolation of sgs2 and sgs3 Arabidopsis mutants impaired in PTGS. We establish a mechanistic link between PTGS, quelling, and RNAi since the Arabidopsis SGS2 protein is similar to an RNA-dependent RNA polymerase like N. crassa QDE-1, controlling quelling, and C. elegans EGO-1, controlling RNAi. In contrast, SGS3 shows no significant similarity with any known or putative protein, thus defining a specific step of PTGS in plants. Both sgs2 and sgs3 mutants show enhanced susceptibility to virus, definitively proving that PTGS is an antiviral defense mechanism that can also target transgene RNA for degradation.

Therapeutic target discovery using Caenorhabditis elegans

Use of the human genome sequence in disease therapy will require efficient identification of disease-causing and disease-associated genes with functions that are amenable to pharmacological manipulation. The validation and development of such genes as therapeutic targets requires information about both the genes' functions and the biochemical pathways in which they participate. One powerful means of obtaining such information is the study of homologous genes in model organisms amenable to laboratory manipulation. Among model organisms the nematode Caenorhabditis elegans offers several advantages, including well-established techniques for genetic and experimental manipulation and the first completed genome sequence for a multicellular organism. Molecular genetic experiments using C. elegans can contribute at several levels to drug discovery programs, from elucidation of genetic functions and pathways to the validation of candidate targets. Additionally, the ease of culture allows adaptation of the nematode for use in high-throughput chemical screens for the identification of lead compounds in drug development.

Making noise about silence: repression of repeated genes in animals

Repeated copies of genes, whether in tandem or dispersed, are often recognized by the cell and silenced. Tandem repeat silencing is associated with a heterochromatin-like complex. Dispersed gene silencing can be mediated by the repressive Polycomb Group complex or involve post-transcriptional silencing presumably involving double-stranded RNA. The I retrotransposable element in Drosophila appears to be susceptible to dispersed gene silencing, potentially by both post-transcriptional and transcriptional processes. Some mutations that eliminate RNA interference in Caenorhabditis elegans result in the mobilization of many transposons and two of these mutations desilence tandem repeats in the germline. One challenge for the future is to determine the nature of any relationship between post-transcriptionally and transcriptionally based mechanisms. The silencing mechanisms potentially act as a protection against high expression of transposons and viruses.

RNA interference: genetic wand and genetic watchdog

In many species, introduction of double-stranded RNA (dsRNA) induces potent and specific gene silencing, a phenomenon called RNA interference or RNAi. The apparently widespread nature of RNAi in eukaryotes, ranging from trypanosome to mouse, has sparked great interest from both applied and fundamental standpoints. Here we review the technical improvements being made to increase the experimental potential of this technique. We also discuss recent advances in uncovering the proteins that act during the RNAi process, discoveries that have revealed enticing links between transposition, transgene silencing and RNAi.

Nematode functional genomics

Alan Coulson has two main roles at the Sanger Centre, revolving around the worm and the human genome projects. Although the worm sequence is essentially finished, the tidying-up of that and the physical map is ongoing. There is also a continuous need for communication with the worm field with regard to information and materials relating to the sequence project. For example, the cosmids and YACs of the physical map continue to be, as they have been for many years now, an extremely powerful resource, and the Sanger Centre distributes in the order of 500 clones per month to the community.

Alan is team leader of the worm functional genomics group, which is currently small but will be expanding shortly. Patricia Kuwabara is a member of the team and a description of their activities can be found below. The Human Genome Project is sequencing mapped PAC and BAC clones. Alan's primary involvement is with the team that is responsible for subcloning the 10 000 or so clones that will be required to complete the one-third of the genome sequence to be contributed by the Sanger Centre.

Patricia Kuwabara has been using Caenorhabditis elegans as a model for understanding how protein–protein interactions regulate cell-to-cell signalling. Her research has focused on understanding the molecular mechanisms underlying the genetics of C. elegans sex determination. This work has led into a study of regulated proteolysis involving calpains and also into the roles of the multiple C. elegans Patched proteins, which in other organisms have been shown to be receptors for the Hedgehog morphogen.

In addition, the group is taking advantage of the completion of the C. elegans genome sequence to develop whole genome DNA microarrays for expression profiling. At the Sanger Centre, DNA microarrays are providing opportunities to examine how development and physiology are regulated globally, because most nematode genes have now been identified at the sequence level. The group are being assisted in this endeavour by Dr Stuart Kim (Stanford, CA).