When compared to the situation in bacteria, transcription regulation in eukaryotes involves many more proteins and much longer stretches of DNA. It often seems bewilderingly complex. Yet many of the same principles apply. As in bacteria, the time and place that each gene is to be transcribed is specified by its cis-regulatory sequences, which are “read” by the transcription regulators that bind to them. Once bound to DNA, positive transcription regulators (activators) help RNA polymerase begin transcribing genes, and negative regulators (repressors) block this from happening. In bacteria, as we have seen, most of the interactions between DNA-bound transcription regulators and RNA polymerases (whether they activate or repress transcription) are direct. In contrast, these interactions are almost always indirect in eukaryotes: many intermediate proteins, including the his-tones, act between the DNA-bound transcription regulator and RNA polymerase. Moreover, in multicellular organisms, it is common for dozens of transcription regulators to control a single gene, with cis-regulatory sequences spread over tens of thousands of nucleotide pairs. DNA looping allows the DNA-bound regulatory proteins to interact with each other and ultimately with RNA polymerase at the promoter. Finally, because nearly all of the DNA in eukaryotic organisms is compacted by nucleosomes and higher-order structures, transcription initiation in eukaryotes must overcome this inherent block.
In the next sections, we discuss these features of transcription initiation in eukaryotes, emphasizing how they provide extra levels of control not found in bacteria.
A eukaryotic Gene Control region Consists of a promoter plus Many cis-regulatory Sequences
In eukaryotes, RNA polymerase II transcribes all the protein-coding genes and many noncoding RNA genes, as we saw in Chapter 6. This polymerase requires five general transcription factors (27 subunits in toto; see Table 6–3, p. 311), in contrast to bacterial RNA polymerase, which needs only a single general transcription factor (the σ subunit). As we have seen, the stepwise assembly of the general transcription factors at a eukaryotic promoter provides, in principle, multiple steps at which the cell can speed up or slow down the rate of transcription initiation in response to transcription regulators.
Because the many cis-regulatory sequences that control the expression of a typical gene are often spread over long stretches of DNA, we use the term gene control region to describe the whole expanse of DNA involved in regulating and initiating transcription of a eukaryotic gene. This includes the promoter, where the general transcription factors and the polymerase assemble, plus all of the cis-regulatory sequences to which transcription regulators bind to control the rate of the assembly processes at the promoter (Figure 7–17). In animals and plants, it is not unusual to find the regulatory sequences of a gene dotted over stretches of DNA as large as 100,000 nucleotide pairs. Some of this DNA is transcribed (but not translated), and we discuss these long noncoding RNAs (lncRNAs) later in this chapter. For now, we can regard much of this DNA as “spacer” sequences that transcription regulators do not directly recognize. It is important to keep in mind that, like other regions of eukaryotic chromosomes, most of the DNA in gene control regions is packaged into nucleosomes and higher-order forms of chromatin, thereby compacting its overall length and altering its properties.
In this chapter, we shall loosely use the term gene to refer to a segment of DNA that is transcribed into a functional RNA molecule, one that either codes for a protein or has a different role in the cell (see Table 6–1, p. 305). However, the classical view of a gene includes the gene control region as well, since mutations in it can produce an altered phenotype. Alternative RNA splicing further complicates the definition of a gene—a point we shall return to later.