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III catalyse the synthesis of rRNA (I), tRNA and snRNA (III). Many non-expressed genes

tend to have residues that are methylated, usually the C of a GC dinucleotide, and in

general active genes tend to be hypomethylated. This is especially prevalent at the

50 flanking regions and is a useful means of discovering and identifying new genes.

5.5.4 Promoter and terminator sequences in DNA

Promoters are usually to the 5^0 end or upstream of the structural gene and have been

best characterised in prokaryotes such asEscherichia coli. They comprise two highly

conserved sequence elements: theTATA box(consensus sequence ‘TATATT’) which is

centred approximately 10 bp upstream from the transcription initiation site (10 in

the gene numbering system), and a ‘GC-rich’ sequence which is centred about25 bp

upstream from the TATA box. The GC element is thought to be important in the initial

recognition and binding of RNA polymerase to the DNA, while the10 sequence is

involved in the formation of a transcription initiation complex (Fig. 5.15a).

The promoter elements serve as recognition sites for DNA binding proteins that

control gene expression and these proteins are termedtranscription factorsortrans-

acting factors. These proteins have a DNA binding domain for interaction with

promoters and an activation domain to allow interaction with other transcription

factors. A well-studied example of a transcription factor is TFIID which binds to the

35 promoter sequence in eukaryotic cells. Gene regulation occurs in most cases at

the level of transcription, and primarily by the rate of transcription initiation,

although control may also be by modulation of mRNA stability, or at other levels

such as translation. Terminator sequences are less well characterised, but are thought

to involve nucleotide sequences near the end of mRNA with the capacity to form a

hairpin loop, followed by a run of U residues, which may constitute a termination

signal for RNA polymerase.

In the case of eukaryotic genes numerous short sequences spanning several hun-

dred bases may be important for transcription, compared to normally less than 100 bp

for prokaryotic promoters. Particularly critical is the TATA box sequence, located

approximately35 bp upstream of the transcription initiation point in the majority of

genes (Fig. 5.15b). This is analogous to the10 sequence in prokaryotes. A number

Translation start site

Transcription start site

Promoter regions

+ strand 5

• strand 3

‘Upstream’

+1

Structural

gene Stop site

Terminator

regions

3 

5 

‘Downstream’

Fig. 5.14Structure and nomenclature of a typical gene.

155 5.5 Functions of nucleic acids