Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

392 Chapter 7: Control of Gene Expression
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.
Summary
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.
MOLECULAR GENETIC MECHANISMS THAT CREATE
AND MAINTAIN SPECIALIZED CELL TYPES
Although all cells must be able to switch genes on and off in response to changes
in their environments, the cells of multicellular organisms have evolved this
capacity to an extreme degree. In particular, once a cell in a multicellular organism
becomes committed to differentiate into a specific cell type, the cell maintains
this choice through many subsequent cell generations, which means that
it remembers the changes in gene expression involved in the choice. This phenomenon
of cell memory is a prerequisite for the creation of organized tissues and
for the maintenance of stably differentiated cell types. In contrast, other changes
in gene expression in eukaryotes, as well as most such changes in bacteria, are
only transient. The tryptophan repressor, for example, switches off the tryptophan
genes in bacteria only in the presence of tryptophan; as soon as tryptophan is
removed from the medium, the genes are switched back on, and the descendants
of the cell will have no memory that their ancestors had been exposed to tryptophan.
In this section, we shall examine not only cell memory mechanisms, but
also how gene regulatory devices can be combined to create the “logic circuits”
through which cells integrate signals and remember events in their past. We begin
by considering one such complex gene control region in detail.
Complex Genetic Switches That Regulate Drosophila
Development Are Built Up from Smaller Molecules
We have seen that transcription regulators can be positioned at multiple sites
along long stretches of DNA and that these proteins can bring into play coactivators
and co-repressors. Here, we discuss how the numerous transcription regulators
that are bound to the control region of a gene can cause the gene to be
transcribed at the proper place and time.