Initiation of transcription is a crucial regulation point for
both prokaryotic and eukaryotic gene expression. Although
some of the same regulatory mechanisms are
used in both systems, there is a fundamental difference
in the regulation of transcription in eukaryotes andbacteria.
We can define a transcriptional ground state as the
inherent activity of promoters and transcriptional machinery
in vivo in the absence of regulatory sequences.
In bacteria, RNA polymerase generally has access to
every promoter and can bind and initiate transcription
at some level of efficiency in the absence of activators
or repressors; the transcriptional ground state is therefore
nonrestrictive. In eukaryotes, however, strong promoters
are generally inactive in vivo in the absence of
regulatory proteins; that is, the transcriptional ground
state is restrictive. This fundamental difference gives
rise to at least four important features that distinguish
the regulation of gene expression in eukaryotes from
that in bacteria.
First, access to eukaryotic promoters is restricted
by the structure of chromatin, and activation of transcription
is associated with many changes in chromatin
structure in the transcribed region. Second, although
eukaryotic cells have both positive and negative regulatory
mechanisms, positive mechanisms predominate in
all systems characterized so far. Thus, given that the
transcriptional ground state is restrictive, virtually every
eukaryotic gene requires activation to be transcribed.
Third, eukaryotic cells have larger, more complex multimeric
regulatory proteins than do bacteria. Finally,
transcription in the eukaryotic nucleus is separated
from translation in the cytoplasm in both space and
time.
The complexity of regulatory circuits in eukaryotic
cells is extraordinary, as the following discussion shows.
We conclude the section with an illustrated description
of one of the most elaborate circuits: the regulatory cascade
that controls development in fruit flies
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