trans

48 TRANSCRIPTION
and RNA pol III synthesizes other small RNAs,
including tRNAs, 5S rRNA, and U6 snRNA.
Eukaryotic RNA pols are multi-subunit enzymes
consisting of 12 or more different polypeptides.
The largest subunit (160–220 kDa), the
second largest subunit (115–135 kDa) and
a third polypeptide with a size of approximately
40 kDa represent the core-enzyme subunits;
they contain highly conserved sequence
motifs with homology to prokaryotic RNA pol
domains and presumably form the active
center of the enzyme. The other subunits are
either specific for a particular RNA pol or common
to two or to all three enzymes. Eukaryotic
RNA pols are unable to recognize specific DNA
sequence motifs and cannot accurately transcribe
genes by themselves. For correct transcription
initiation, auxiliary factors are needed
which assemble on promoter sequences and, by
recruiting the RNA pol, form a stable transcription
initiation complex. Each RNA pol interacts
with a specific set of transcription factors and,
therefore, depends on characteristic promoter
structures. Accordingly, eukaryotic genes are
divided into class I, class II, or class III genes.
Some factors take part in transcription of genes
belonging to different classes. The most prominent
example of a ubiquitous factor is the TATAbox
binding protein (TBP), a single polypeptide
that, as a component of various multi-subunit
transcription factors, is important for transcription
initiation of all three RNA pols. Auxiliary
factors and RNA pol in conjunction with a functional
promoter are able to direct a basal level of
correctly initiated transcription and constitute
the general or basal transcription machinery. In
addition, several groups of transcription regulators
and cofactors have been described which
modulate transcription efficiency at the level of
transcription initiation. In the nucleus, the DNA
is organized as chromatin, and the nucleosomal
structure formed by histones is a general transcription
repressor because it obstructs the
interaction of the basal transcription machinery
with the promoter region. Therefore, chromatin
remodeling is an essential step for
efficient transcription initiation at chromatin
templates. After transcription initiation, the
RNA pol detaches from the auxiliary factors,
escapes from the promoter, and transforms
into a transcription elongation complex. Transcription
then proceeds until a termination
signal is encountered. Each RNA pol has its
specific signal and termination mode. RNA
pol III terminates at short runs of 4 to 7 T
residues in the sense strand, independent of a
trans-acting factor. In contrast, termination
determinants of class I genes bind a protein
factor which, by specifically interacting with
RNA pol I, disrupts transcription. Termination
of RNA pol II transcription is less well characterized,
but it requires G-rich sequences and,
in the case of mRNA synthesis, appears to be
coupled to RNA polyadenylation.
UNUSUAL MODES OF
TRANSCRIPTION IN
TRYPANOSOMATIDS AND
NEMATODES
Polycistronic transcription of protein
coding genes
In eukaryotes, a protein coding gene typically
constitutes a single transcription unit, i.e. it
is transcribed monocistronically. Cotranscriptional
capping of mRNA, a process in which a
7-methylguanosine triphosphate is fused in a
5–5 linkage to nascent pre-mRNAs, appears
to be the main reason for this mode of
transcription because the capping enzyme
requires a free 5 end. Nonetheless, several
polycistronic transcripts have been identified
in higher eukaryotes, but, characteristically,
these molecules mature as polycistronic units.
MOLECULAR BIOLOGY