GENERAL TRANSCRIPTION FACTORS, RNA POLYMERASE, MEDIATOR, CHROMATIN REMODELING COMPLEXES, AND HISTONE-MODIFYING ENZYMES
RNA polymerase bound to histone-modifying enzymes. As discussed in Chapter 4, both types of enzymes can increase access to the DNA in chromatin, and by doing so they facilitate the assembly of the transcription initiation machinery onto DNA.
As illustrated in Figure 6–18, many proteins (well over 100 individual subunits) must assemble at the start point of transcription to initiate transcription in a eukaryotic cell. The order of assembly of these proteins does not seem to follow a prescribed pathway; rather, the order differs from gene to gene. Indeed, some of these different protein complexes may be brought to DNA as preformed subassemblies.
To begin transcribing, RNA polymerase II must be released from this large complex of proteins. In addition to the steps described in Figure 6–14, this release often requires the in situ proteolysis of the activator protein. We shall return to some of these issues, including the role of chromatin remodeling complexes and histone-modifying enzymes, in Chapter 7, where we discuss how eukaryotic cells regulate the process of transcription initiation.
Once RNA polymerase has initiated transcription, it moves jerkily, pausing at some DNA sequences and rapidly transcribing through others. Elongating RNA polymerases, both bacterial and eukaryotic, are associated with a series of elongation factors, proteins that decrease the likelihood that RNA polymerase will dissociate before it reaches the end of a gene. These factors typically associate with RNA polymerase shortly after initiation and help the polymerase move through the wide variety of different DNA sequences that are found in genes. Eukaryotic RNA polymerases must also contend with chromatin structure as they move along a DNA template, and they are typically aided by ATP-dependent chromatin remodeling complexes that either move with the polymerase or may simply seek out and rescue the occasional stalled polymerase. In addition, histone chaperones help by partially disassembling nucleosomes in front of a moving RNA polymerase and assembling them behind.
As RNA polymerase moves along a gene, some of the enzymes bound to it modify the histones, leaving behind a record of where the polymerase has been. Although it is not clear exactly how the cell uses this information, it may aid in
Figure 6–18 Transcription initiation by RNA polymerase II in a eukaryotic cell.
Transcription initiation in vivo requires the presence of transcription activator proteins. As described in Chapter 7, these proteins bind to specific short sequences in DNA. Although only one is shown here, a typical eukaryotic gene utilizes many transcription activator proteins, which in combination determine its rate and pattern of transcription. Sometimes acting from a distance of several thousand nucleotide pairs (indicated by the dashed DNA molecule), these proteins help RNA polymerase, the general transcription factors, and Mediator all to assemble at the promoter. In addition, activators attract ATP-dependent chromatin remodeling complexes and histone-modifying enzymes. One of the main roles of Mediator is to coordinate the assembly of all these proteins at the promoter so that transcription can begin. As discussed in Chapter 4, the “default” state of chromatin is a condensed fiber (see Figure 4–28), and this is likely to be the form of DNA upon which most transcription is initiated. For simplicity, the chromatin is not shown in this figure.
transcribing a gene over and over again once it has become active for the first time. It may also be used to coordinate transcription elongation with the processing of RNA as it emerges from RNA polymerase, a topic we discuss later in this chapter.