To avoid such cross-talk, several types of DNA elements compartmentalize the genome into discrete regulatory domains. In Chapter 4, we discussed barrier sequences that prevent the spread of heterochromatin into genes that need to be expressed. A second type of DNA element, called an insulator, prevents cis-regulatory sequences from running amok and activating inappropriate genes (Figure 7–24). Insulators function by forming loops of chromatin, an effect mediated by specialized proteins that bind them (see Figures 4–48 and 7–24B). The loops hold a gene and its control region in rough proximity and help to prevent the control region from “spilling over” to adjacent genes. Importantly, these loops can be in different in different cell types, depending on the particular proteins and chromatin structures that are present.
The distribution of insulators and barrier sequences in a genome is thought to divide it into independent domains of gene regulation and chromatin structure (see pp. 207–208). Aspects of this organization can be visualized by staining whole chromosomes for the specialized proteins that bind these DNA elements (Figure 7–25).
Figure 7–25 Localization of a Drosophila insulator-binding protein on polytene chromosomes.
A polytene chromosome (discussed in Chapter 4) was stained with propidium iodide (red) to show its banding patterns, with bands appearing bright red and interbands as dark gaps in the pattern (top). the positions on this polytene chromosome that are bound by a particular insulator protein are stained bright green using antibodies directed against the protein (bottom). this protein is preferentially localized to interband regions, reflecting its role in organizing chromosomes into structural, as well as functional, domains. for convenience, these two micrographs of the same polytene chromosome are arranged as mirror images. (Courtesy of Uli laemmli, from K. Zhao et al., Cell 81:879–889, 1995. with permission from elsevier.)
Although chromosomes are organized into orderly domains that discourage control regions from acting indiscriminately, there are special circumstances where a control region located on one chromosome has been found to activate a gene located on a different chromosome. Although there is much we do not understand about this mechanism, it indicates the extreme versatility of transcriptional regulation strategies.
Transcription regulators switch the transcription of individual genes on and off in cells. In prokaryotes, these proteins typically bind to specific DNA sequences close to the RNA polymerase start site and, depending on the nature of the regulatory protein and the precise location of its binding site relative to the start site, either activate or repress transcription of the gene. The flexibility of the DNA helix, however, also allows proteins bound at distant sites to affect the RNA polymerase at the promoter by the looping out of the intervening DNA. The regulation of higher eukaryotic genes is much more complex, commensurate with a larger genome size and the large variety of cell types that are formed. A single eukaryotic gene is typically controlled by many transcription regulators bound to sequences that can be tens or even hundreds of thousands of nucleotide pairs from the promoter that directs transcription of the gene. Eukaryotic activators and repressors act by a wide variety of mechanisms—generally altering chromatin structure and controlling the assembly of the general transcription factors and RNA polymerase at the promoter. They do this by attracting coactivators and co-repressors, protein complexes that perform the necessary biochemical reactions. The time and place that each gene is transcribed, as well as its rates of transcription under different conditions, are determined by the particular spectrum of transcription regulators that bind to the regulatory region of the gene.