trans

60 TRANSCRIPTION
FIGURE 3.2 Comparison of SL RNA and U1 snRNA
gene promoters. Schematic drawing to scale of SL
RNA or U1 snRNA (U1) gene promoters of human,
Ascaris lumbricoides, Leptomonas seymouri and
Leishmania tarentolae. Promoters are aligned according
to TISs, indicated by flags, and promoter elements
are represented by rectangles. In the parasite promoters,
elements which have been shown to specifically
interact with essential transcription factors are drawn
in black. DSE stands for distal sequence element, PSE
for proximal sequence element, IPE for intragenic
promoter element, and Inr for initiator element. The
position of the DSE in the human U1 promoter is
given relative to the TIS.
was found to be important for transcription
termination and correct U snRNA 3 end formation.
However, recent data suggest that
transcription terminates further downstream.
The U6 snRNA gene promoter shares PSE
and DSE with other U snRNA gene promoters
but has an additional TATA-box downstream
of the PSE which confers specificity for RNA
pol III.
SL RNA and U1 snRNA gene
transcription in Ascaris lumbricoides
In the nematode parasite A. lumbricoides, the
development of an in vitro transcription system
has enabled a detailed analysis of the SL
RNA gene structure. In this organism, SL RNA
and 5S rRNA genes are present on the same
tandem repeat unit and are transcribed in the
same orientation. The sequence between the
5S rRNA and SL RNA coding regions contains
a single short SL RNA gene promoter element
centered at position 50, similar to the PSE of
human U snRNA genes (Figure 3.2). In vitro
assays failed to detect a DSE in the SL RNA gene
promoter but identified an essential second
element just downstream of the TIS comprising
the 22-bp SL sequence itself. Transcription and
parallel DNase I footprinting experiments indicated
that SL RNA gene transcription depends
on the binding of a transcription factor to the
intragenic promoter element (IPE). Accordingly,
gel shift assays revealed specific band-shifts
with a double-stranded DNA probe spanning
the IPE and, by DNA affinity chromatography, a
polypeptide of 60 kDa was isolated that binds
the IPE in a zinc-dependent manner. Since the
IPE is conserved among nematode species but
not found in mammalian U snRNA gene promoters,
it is possible that the IPE-binding protein
is a nematode-specific transcription factor.
Furthermore, it is likely to be a gene-specific
factor as well, because in vitro characterization
of the A. lumbricoides U1 snRNA gene promoter
revealed a PSE at the same position as in the SL
RNA gene promoter but no IPE (Figure 3.2). The
PSEs of both promoters have no obvious consensus
sequence and it remains to be determined
whether they interact with common or
specific transcription factors. The SL RNA gene
contains a sequence element 12 bp downstream
of its coding region which closely resembles a
mammalian 3 box. Mutation of this sequence
MOLECULAR BIOLOGY