Biology Reference
In-Depth Information
charged DNA molecule through basic amino acid residues. Activation domains of
transcription factors also come in four types: rich in either glutamine, proline,
serine/threonine, or acidic amino acids. Examples of these types are SP1,
CTF/NF-1, Pit-1, and GATA-1, respectively (reviewed by Ptashne, 1988; Ptashne
and Gann, 1990).
Transcriptional repressor proteins may bind directly to DNA or exert their
repressive effects indirectly by interacting with basal transcription factors, tran-
scriptional activators and co-repressor proteins to inhibit transcription by RNA
polymerases (Hanna-Rose and Hansen, 1996).
The study of DNA-protein interactions has been enormously facilitated by the
use of two techniques: gel retardation analysis (also termed band or mobility shift
assays; Dent and Latchman, 1993) and DNase I footprinting (Lakin, 1993). The
former technique is extremely useful for searching for DNA-binding proteins in
crude nuclear extracts whereas the latter method provides information as to the
precise location of the binding site on the DNA sequence under study.
5
UTR; the sequence lying between the transcriptional initiation site and the
translational start codon, ATG;
Figure 1.1
) is often essential for the normal
expression of a gene. Sequences in the 5
and 3
untranslated regions.
The presence of the 5
untranslated region (5
UTRs of various genes are thought to
play a role in controlling the translation of the encoded mRNA (reviewed by
Curtis
et al
., 1995; Melefors and Hentze, 1993; Pesole
et al
., 1997; Sachs, 1993).
Perhaps the best characterized posttranscriptional control mechanism involving
the 5
UTR is that of the iron response element (IRE). The IRE is found in the
5
UTRs of several human genes [e.g. ferritin (
FTH1
), transferrin (
TF
), erythroid
5-aminolevulinate acid synthase (
ALAS1
); Cox and Adrian 1993; Bhasker
et al
.,
1993] and is capable of adopting a stem-loop structure that interacts with a
cytosolic RNA-binding protein thereby inhibiting mRNA translation. The post-
transcriptional regulation of several other human genes [e.g. transforming
growth factor-
1 (
TGFB1
; Kim
et al
., 1992b) and basic fibroblast growth factor
(
FGF2
; Prats
et al
., 1992)] also appears to involve regulatory elements that mod-
ulate the efficiency of translation.
Zhang (1998) examined the nature of translational start codons in human
genes. The relative frequencies of start codons occurring as the first, second, third
or fourth ATG codons in the reading frame were 474, 51, 5, and 0, respectively.
There are, however, quite a few examples of more than one ATG being used in the
same gene. Thus, the alternative use of two ATG codons 84 bp apart in the human
peroxisome proliferator-activated receptor (
PPARG
; 3p25) gene serves to gener-
ate two distinct protein isoforms that differ in length by 28 amino acids at the
amino terminal end of the protein (Elbrecht
et al
., 1996). The alternative use of
different ATG initiation codons has also been reported for the human von Hippel
Lindau (
VHL
; 3p25-p26) gene which leads to the production of two distinct pro-
tein products that differ in length by 53 amino acids (Blankenship
et al
., 1999).
Zhang (1998) reported that the ratio of the frequencies of stop codons TAA,
TAG and TGA in human genes was about 1:1:2. The 3
untranslated region is
that region of a gene which lies downstream of the stop codon. The AATAAA
sequence located downstream of the stop codon (TAA in
Figure 1.1
) of ~90% of
