How and Why Do Plants Inactivate Homologous (Trans)genes?

Abstract

Gene silencing in transgenic plants has emerged in the last 5 years as a topic of intense interest for both applied and basic plant scientists. From the applied side, gene silencing has come as an unwelcome surprise. Early reviews of the prospects for plant genetic engineering did not pinpoint this as a potential obstacle. Rather, the anticipated challenge was to identify tissueand stage-specific promoters that could be used to obtain regulated transgene expression. Yet, silencing of transgenes is turning out to be a substantial problem, as described recently in an aptly titled review, Transgene Inactivation: Plants Fight Back! (Finnegan and McElroy, 1994). According to this article, of 30 companies polled, nearly all reported some problems with unwanted silencing of transgenes. While companies are struggling to find ways to avoid silencing, a small cadre of basic scientists has become fascinated by the phenomenon and is analyzing a variety of silencing systems. To this latter group, the phenomenon of silencing represents more than just an unwanted response to foreign genes; rather, it has opened a door that might lead to a deeper understanding of previously unsuspected ways that plants naturally use homologous or complementary nucleic acid sequences to modify gene expression, both in the nucleus at the DNA level and in the nucleus or cytoplasm as a means to control excess production of mRNA or replication of RNA pathogens. Initial studies of transgenic plants concentrated on those showing tissue-specific and/or high levels of expression. Plants that did not exhibit the desired expression characteristics were usually discarded. It was only a matter of time, however, until such plants would begin to be treated as objects of scientific investigation in their own right. In the late 1980s, papers started to appear that were devoted solely to describing cases of silencing that involved transgene/transgene or transgene/endogenous gene interactions. A central feature of all of these studies was that silencing was associated with multiple copies of homologous DNA sequences, which could comprise protein-coding regions, promoters, or both. Although the initial impulse was to lump these first cases together as a single phenomenon, it has since become clear that several different mechanisms are probably involved. These different mechanisms are united, however, in the sense that they all involve variations on nucleic acid interactions: DNA-DNA, RNA-RNA, and DNA-RNA. A general term that encompasses all of these phenomena is homology-dependent gene silencing. Numerous detailed reviews of this topic are available (Jorgensen, 1992; Matzke and Matzke, 1993; Flavell, 1994; Matzke et al., 1994b; Mol et al., 1994).