1. Introduction

21.14 Summary

Some regulatory promoter elements are present in many genes and are recognized by ubiquitous factors; others are present in a few genes and are recognized by tissue-specific factors. Elements that uniquely identify particular groups of genes that are regulated in response to certain transcription factors are called response elements (REs). Binding of factors to specific sequences is followed by protein-protein interactions with other components of the general transcription apparatus. Transcription factors often have a modular construction, in which there are independent domains responsible for binding to DNA and for activating transcription. The main function of the DNA-binding domain may be to tether the activating domain in the vicinity of the initiation complex.

Several groups of transcription factors have been identified by sequence homologies. The homeodomain is a 60 residue sequence found in genes that regulate development in insects and worms and in mammalian transcription factors. It is related to the prokaryotic helix-turn-helix motif and provides the motif by which the factors bind to DNA.

Another motif involved in DNA-binding is the zinc finger, which is found in proteins that bind DNA or RNA (or sometimes both). A finger has cysteine residues that bind zinc. One type of finger is found in multiple repeats in some transcription factors; another is found in single or double repeats in others.

Steroid receptors were the first members identified of a group of transcription factors in which the protein is activated by binding a small hydrophobic hormone. The activated factor becomes localized in the nucleus, and binds to its specific response element, where it activates transcription. The DNA-binding domain has zinc fingers.

The leucine zipper contains a stretch of amino acids rich in leucine that are involved in dimerization of transcription factors. An adjacent basic region is responsible for binding to DNA.

HLH (helix-loop-helix) proteins have amphipathic helices that are responsible for dimerization, adjacent to basic regions that bind to DNA.

Many transcription factors function as dimers, and it is common for there to be multiple members of a family that form homodimers and heterodimers. This creates the potential for complex combinations to govern gene expression. In some cases, a family includes inhibitory members, whose participation in dimer formation prevents the partner from activating transcription.

The existence of a preinitiation complex signals that the gene is in an "active" state, ready to be transcribed. The complex is stable, and may remain in existence through many cycles of replication. The ability to form a preinitiation complex could be a general regulatory mechanism. By binding to a promoter to make it possible for RNA polymerase in turn to bind, the factor in effect switches the gene on.

The variety of situations in which hypersensitive sites occur suggests that their existence reflects a general principle. Sites at which the double helix initiates an activity are kept free of nucleosomes. A transcription factor, or some other nonhistone protein concerned with the particular function of the site, modifies the properties of a short region of DNA so that nucleosomes are excluded. The structures formed in each situation need not necessarily be similar (except that each, by definition, creates a site hypersensitive to DNAase I).

Genes whose control regions are organized in nucleosomes usually are not expressed. In the absence of specific regulatory proteins, promoters and other regulatory regions are organized by histone octamers into a state in which they cannot be activated. This may explain the need for nucleosomes to be precisely positioned in the vicinity of a promoter, so that essential regulatory sites are appropriately exposed. Some transcription factors have the capacity to recognize DNA on the nucleosomal surface, and a particular positioning of DNA may be required for initiation of transcription.

Acetylation of histones occurs at both replication and transcription and could be necessary to form a less compact chromatin structure. Some coactivators, which connect transcription factors to the basal apparatus, have histone acetylase activity. Conversely, repressors may be associated with deacetylases.

Active chromatin and inactive chromatin are not in equilibrium. Sudden, disruptive events are needed to convert one to the other. Chromatin remodeling complexes have the ability to displace histone octamers by a mechanism that involves hydrolysis of ATP. A typical form of this chromatin remodeling is to displace one or more histone octamers from specific sequences of DNA, creating a boundary that results in the precise or preferential positioning of adjacent nucleosomes. Chromatin remodeling may also involve changes in the positions of nucleosomes.

A group of hypersensitive sites upstream of the cluster of β-globin genes forms a locus control region (LCR) that is required for expression of all of the genes in the domain. The ends of domains may be marked by sequences that block the transmission of regulatory effects. Domains may also possess sites for attachment to the nuclear matrix.

CpG islands contain concentrations of CpG doublets and often surround the promoters of constitutively expressed genes, although they are also found at the promoters of regulated genes. The island including a promoter must be unmethylated for that promoter to be able to initiate transcription. A specific protein binds to the methylated CpG doublets and prevents initiation of transcription.

The formation of heterochromatin occurs by proteins that bind to specific chromosomal regions (such as telomeres) and that interact with histones. The formation of an inactive structure may propagate along the chromatin thread from an initiation center. Similar events occur in silencing of the inactive yeast mating type loci. Repressive structures that are required to maintain the inactive states of particular genes are formed by the Pc-G protein complex in Drosophila. They share with heterochromatin the property of propagating from an initiation center.