382
Cell Nucleus Biogenesis, Structure and Function
adaptor proteins that interact with these
factors. Genetic elements within the gene
promoters deFne where the transcription
will begin. General transcription factors
play a fundamental role in this process. ±or
most eukaryotic promoters, the process is
activated by association of the factor T±IID
with DNA. T±IID is a large multiprotein
complex, one subunit of which, the TATA
sequence
binding
protein
(TBP),
can
recognize and associate with the canonical
promoter element TATA. T±IID bound
to the promoter can then activate the
sequential recruitment of other factors as
follows: T±IIB; T±IIE with T±II± and RNA
polymerase; T±IIH. Once assembly of
this preinitiation complex is complete, the
T±IIH complex directs phosphorylation of
a domain of the RNA polymerase complex
called the
C-terminal domain
(CTD). The
CTD is conserved in eukaryotic RNA
polymerase II proteins. The mammalian
enzyme has 52 repeats of the amino acid
(consensus) sequence YSPTSPS, in which
the serine (S) and threonine (T) residues
can be phosphorylated. Phosphorylation
of the CTD correlates with release of the
synthetic complex from the promoter and
the initiation of RNA synthesis. During
synthesis, the DNA template is used to
generate a corresponding RNA molecule,
which is polymerized from its 5
0
toward
its 3
0
end. The 3
0
end of the transcript
is generated by a process that cuts the
nascent RNA and adds a poly(A) tail.
This process recognizes a set of sequence
elements in the RNA that interact with
the poly(A) synthesis machinery. Once
the nascent RNA is processed in this
way, the engaged polymerase complex is
destabilized so that it will soon dissociate
from the template – this termination step
appears not to be directed by a speciFc
sequence in DNA and is thought to be
more probabilistic, so that the polymerase
‘‘drops off’’ the DNA at some point within
a few kbp at the end of the gene.
2.1.2
Specifc Transcription Factors
The general transcription factors provide
only part of the mechanism that regulates
gene expression in higher eukaryotes. In
multicellular organisms, it is clear that
complex mechanisms of regulation are re-
quired to ensure that particular genes are
exp
ressedinthedes
i
redce
l
lsanda
tthe
appropriate times of development. This
function is performed by speciFc tran-
scription factors. As the name implies,
speciFc transcription factors function to
activate transcription from a single gene or
a group of genes with similar expression
characteristics. As a general rule, genes
that are expressed in a speciFc cell lin-
eage will only be expressed in cells with
the appropriate constellation of transcrip-
tion factors. Certain speciFc transcription
factors will play a dominant role in main-
taining the active chromatin status across
target genes. Others will activate or en-
hance levels of gene expression beyond
the levels that are provided by the general
transcription factors alone.
It is self-evident that this class of tran-
scription factors must achieve speciFcity
by virtue of their interaction with speciFc
DNA elements within target genes. ±or
most factors, the DNA target will lie within
1 to 2 turns of the double helix. These
DNA elements can be located close to
the promoter itself, within promoter prox-
imal activating sequences, but, in many
cases, these are located in transcriptional
enhancer elements that can be as much as
100 kbp for the gene promoter. This sur-
prising observation reflects the fact that
the chromatin itself is flexible and able
to fold, so that the remote sequences and
associated factors can contribute to the
efFciency with which gene expression is
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