Gene activation and gene silencing.

Twenty-five years ago the field of eukaryotic gene regulation was in its infancy. Paradigms driving experiments came primarily from work with prokaryotes and the phage that infected them (12). These paradigms, pioneered by Jacob and Monod, were that genes contained promoter sequences to which RNA polymerase bound and cis-acting sequences to which geneor pathway-specific trans-acting factors bound. The cis-acting sequences typically were located very near to the transcription start site. The function of activators and repressors could be modulated by specific physiological conditions, with their binding influencing the efficiency of RNA polymerase activity in a positive or negative manner. The development of recombinant DNA enabled the cloning of eukaryotic genes, whereas the development of transformation methods allowed the introduction of modified genes, providing tests of these ideas. In this perspective we will focus on the key concepts that have emerged from studies of gene regulation in plants, focusing on regulatory mechanisms operating on nuclear endogenous genes and transgenes. These studies have revealed that the prokaryotic paradigm is applicable, but it is not the complete story. Plant researchers have discovered mechanisms superimposed upon the DNA sequence-mediated controls. Studies of these epigenetic phenomena, transposable element cycling, paramutation, and transgene silencing, have revealed novel, previously unimagined mechanisms operating in eukaryotic cells.