Chapter Introduction

21: The Transcriptional Regulation of Gene Expression in Eukaryotes

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  • 21.1 Basic Mechanisms of Eukaryotic Transcriptional Activation

  • 21.2 Combinatorial Control of Gene Expression

  • 21.3 Transcriptional Regulation Mechanisms Unique to Eukaryotes

MOMENT OF DISCOVERY

Tracy Johnson

Our lab has been trying to understand how pre-mRNA splicing can occur cotranscriptionally, which would neatly tie together the steps in producing functional mRNAs and provide cells with many interesting avenues for gene regulation along the way. Starting with a genetic screen in yeast in which nonessential transcription factors were mutated, we looked for mutations in a second gene that would cause cell death, an effect referred to as synthetic lethal. For a long time we found absolutely nothing interesting. But we kept working, and at last discovered that a deletion of the gene encoding the Gcn5 protein was synthetic lethal when combined with mutations in genes encoding parts of the U2 snRNP component of spliceosomes. Gcn5 is a histone acetyltransferase (HAT), a well-characterized enzyme that adds acetyl groups to histone proteins within nucleosomes, but it had no known connection to pre-mRNA splicing.

The real moment of surprise came when we found that when the GCN5 gene is deleted, cotranscriptional splicing is completely messed up! This is because the U2 snRNP is no longer recruited to pre-mRNA splice sites. The splicing defect is specific to this HAT and requires the enzyme’s catalytic activity, which is targeted toward promoter-bound histones. I never imagined there would be a link between chromatin structure and pre-mRNA splicing, as is implied by this finding. We envision that a specific pattern of histone acetylation leads to physical recruitment of proteins to acetylated histones within chromatin, which in turn recruits spliceosomes to newly transcribed pre-mRNAs. Because the HAT is very well conserved in mammals, it could be a general mechanism that affects which splice sites are chosen in pre-mRNAs, depending on the acetylation state of the histones associated with the parent gene.

—Tracy Johnson, on discovering that pre-mRNA splicing requires specific histone acetylation

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Eukaryotic cells, like bacteria, express only a subset of their genes at any given time. We saw in Chapter 20 that bacteria, through gene regulation, are able to adapt to environmental changes and respond to signaling molecules and viral assaults. Eukaryotes, too, must respond to their environment and external stimuli. But in addition, multicellular eukaryotes must manage complex pathways of cell division and differentiation that give rise to the multitude of cell types required for organismal development. Developmental programs are extremely precise—it is critical that each protein influencing cellular differentiation is active at the right time and in the right place—and any deviation from the program can have drastic consequences. Many of the genes needed for development are so critical that if mutation renders them nonfunctional, the embryo dies before the organism is fully formed. Yet, even though the needs of a eukaryote are more complex than those of a bacterium, basic principles of gene regulation are still the key to all of these processes.

Recall that many bacterial genes and operons are regulated at the level of transcription initiation. This is true in eukaryotes as well, and as we will see, many eukaryotic regulatory mechanisms build on those used in bacteria. However, there is a fundamental difference between bacterial and eukaryotic regulation of transcription. The transcriptional ground state, the inherent activity of promoters and transcription machinery in vivo in the absence of regulatory mechanisms, is not the same in bacteria and eukaryotes. In bacteria, the transcriptional ground state is nonrestrictive; RNA polymerase generally has access to every promoter and can bind and initiate transcription at some level of efficiency in the absence of activators or repressors. In contrast, eukaryotic genes contain strong promoters that are generally inactive in the absence of regulatory proteins—the transcriptional ground state in eukaryotes is restrictive.

Crucial differences in DNA packaging and cell structure give rise to at least four important distinguishing features of regulation of gene expression in eukaryotes. First, access to eukaryotic promoters is restricted by the structure of chromatin, and transcriptional activation is associated with many changes in chromatin structure in the transcribed region. Second, although eukaryotic cells have both positive and negative regulatory mechanisms, positive mechanisms predominate in all systems investigated so far; given that the transcriptional ground state is restrictive, virtually every eukaryotic gene requires activation. Third, eukaryotic cells have larger, more complex, multiprotein regulatory networks than bacteria. And finally, transcription in the nucleus is separated from translation in the cytoplasm, in both space and time. As a result, posttranscriptional control plays a larger role in controlling gene expression in eukaryotes, as we will see in Chapter 22.

The complexity of regulatory circuits in eukaryotic cells is extraordinary, and we will not attempt comprehensive coverage of all aspects. This chapter and the next cover some of the guiding principles of eukaryotic gene regulation, drawing parallels to the mechanisms discussed for bacteria in Chapter 20, wherever applicable. The need to control the multitude of genes in a higher eukaryote requires an array of regulatory proteins for every single gene. We begin by discussing the basic logic of gene activation as used in essentially all eukaryotes. We take a brief look at experiments that first revealed the modular architecture of gene activators and highlight some of the regulatory networks that govern gene expression, from the simple system in yeast to the complex developmental controls typical in a multicellular eukaryote. The chapter concludes with a discussion of transcriptional control processes unique to eukaryotic gene expression, some of which are still far from understood.