Eukaryotic transcriptional regulatory proteins

The past five years have offered a virtual explosion of information in the field of eukaryotic gene regulation. The natural anticipation that a considerable degree of regulation would be imparted at the level of mRNA synthesis (transcription) has been satisfied. When the polypeptide product of a gene is absent from a eukaryotic cell, its absence is typically due to the fact that its encoding gene is transcriptionally inert. There are important and highly interesting exceptions to this general rule, such as the regulated splicing of transcripts synthesized from the various fruit fly genes that control sexual phenotype. However, many lines of evidence identify transcriptions as the most common and immediate focal point of genetic regulation in eukaryotic cells. As in prokaryotic organisms, transcriptional control in eukaryotes results from an interplay between regulatory DNA sequences and site-specific DNA-binding proteins. Transcription of eukaryotic genes is influenced by various regulatory elements, termed promoters, enhancers, and silencers. These elements, in turn, are composed of discrete DNA sequence motifs, which constitute binding sites for sequence-specific DNA-binding proteins. A major effort is now under way to identify sequence-specific DNA-binding proteins, to match them to their cognate sites within or around eukaryotic genes, and to elucidate how the binding of such proteins results in increased or decreased transcription of the associated gene. This review focuses on recent information regarding the nature of eukaryotic transcriptional regulatory proteins, primarily ones that bind to DNA in a sequence-specific manner. Albeit an exciting time, the past several years have also generated a considerable amount of information that has yet to fall into place. We have chosen to concentrate our discussion on a few examples that illustrate particular concepts. Most of these are cases where considerable biochemical information has been obtained, although many of these systems owe their origins to classical genetic studies. The plethora of information concerning gene regulatory proteins can be largely attributed to several methodological advances that have occurred in the past decade. For example, cell-free extracts have been developed that recapitulate accurate transcription from RNA polymerase II promoters using cloned DNA templates. Also, detection of rare DNA-binding activities in crude cell extracts has become possible due to sensitive DNA protection and gel retardation assays. Finally, purification of these proteins has been expedited by the refinement of sequence-specific DNA affinity chromatography techniques. It would be impossible to cover all of the developments in the diverse field of transcriptional regulators. In particular, we have circumvented two important issues that have recently been reviewed elsewhere: how regulatory proteins communicate information to the transcriptional apparatus via activator domains, and the biochemical events involving RNA polymerase II and ancillary factors that occur during transcriptional initiation. We have instead chosen to begin this review by outlining the basic structural motifs that endow proteins the capacity to bind DNA in a sequence-specific manner, then focus on results and observations that were not necessarily anticipated from precedent studies on bacterial gene regulation. We hope to provide a framework for the consideration of topics that qualify as looming enigmas, and present speculations on the importance of protein:protein interactions. Lastly, we address the problem of how transcriptional regulatory proteins are themselves controlled.