We have seen that nuclear receptors respond to signal molecules by recruiting coactivators. Now we can ask, how do coactivators modulate transcriptional activity? Recall that the template for RNA synthesis in eukaryotes is not simply naked DNA; rather, it is a complex of DNA and histones called chromatin. Some proteins that stimulate transcription act to loosen the histone complex from the DNA, exposing additional DNA regions to the transcription machinery. One means by which loosening takes place is with the enzymatic attachment of acetyl groups to histones.

So far in our study of biochemistry, we have seen acetyl CoA only in the context of intermediary metabolism, for instance, as a fuel for the citric acid cycle or as a precursor for fatty acid synthesis and for steroid synthesis. However, acetyl CoA also plays a role in the regulation of gene expression. Recall that citrate is transported out of mitochondria and is cleaved into oxaloacetate and acetyl CoA in the cytoplasm by ATP-citrate lyase. Recent research shows that citrate can also enter the nucleus, where a nuclear ATP-citrate lyase generates acetyl CoA for use as a substrate for histone-modifying enzymes. For instance, some of the p160 coactivators and the proteins that they recruit covalently modify the amino-terminal tails of histones by catalyzing the transfer of acetyl groups from acetyl CoA to specific lysine residues in these amino-terminal tails.

Enzymes that catalyze such reactions are called histone acetyltransferases (HATs). The histone tails are readily extended, so they can fit into the HAT active site and become acetylated (Figure 37.12).

What are the consequences of histone acetylation? Lysine bears a positively charged ammonium group at neutral pH. The addition of an acetyl group neutralizes the ammonium group to an amide group while adding a negative charge. This change dramatically reduces the affinity of the tail for DNA and decreases the affinity of the entire histone complex for DNA, loosening the histone complex from the DNA.

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In addition, the acetylated lysine residues interact with a specific acetyllysine-binding domain, termed a bromodomain, that is present in many proteins that regulate eukaryotic transcription. These domains serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling. Bromodomain-containing proteins are components of two large complexes essential for transcription. One is a complex of more than 10 polypeptides that binds to the TATA-box-binding protein. Recall that TBP is an essential transcription factor for many genes. Proteins that bind to TBP are called TAFs (for TATA-box-binding protein associated factors). In particular, TAF1 contains a pair of bromodomains near its carboxyl terminus. The two domains are oriented such that each can bind one of two acetyllysine residues at positions 5 and 12 in the histone H4 tail. Thus, acetylation of the histone tails provides a mechanism for recruiting other components of the transcriptional machinery.

Bromodomains are also present in some components of large complexes known as chromatin-remodeling engines. These complexes, which also contain domains similar to those of helicases, utilize the free energy of ATP hydrolysis to shift the positions of nucleosomes along the DNA and to induce other conformational changes in chromatin, potentially exposing binding sites for other factors (Figure 37.13). Thus, histone acetylation can activate transcription through a combination of three mechanisms: by reducing the affinity of the histones for DNA, by recruiting other components of the transcriptional machinery, and by initiating the remodeling of the chromatin structure. Acetylation is not the only means of modifying histones. Other means include phosphorylation and methylation (Table 37.3).

Recall that nuclear hormone receptors also include regions that interact with components of coactivators. Thus, two mechanisms of gene regulation can work in concert. The modification of histones and chromatin remodeling can open up regions of chromatin into which the transcription complex can be recruited through protein–protein interactions.

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Just as in bacteria, some changes in a cell’s environment lead to the repression of genes that had been active. The modification of histone tails again plays an important role. However, in repression, a key reaction appears to be the deacetylation of acetylated lysine, catalyzed by specific histone deacetylase enzymes. Indeed, all covalent modifications of histone tails are reversible.

In many ways, the acetylation and deacetylation of lysine residues in histone tails is analogous to the phosphorylation and dephosphorylation of serine, threonine, and tyrosine residues in other stages of signaling processes. Like the addition of phosphoryl groups, the addition of acetyl groups can induce conformational changes and generate novel binding sites. Without a means of removing these groups, however, these signaling switches will become stuck in one position and lose their effectiveness. Like phosphatases, deacetylases help reset the switches.