Download Some transcription factors ("Enhancer

Lecture 7. Regulation of Eukaryotic Gene Expression
1. Eukaryotic Gene structure
A gene is the DNA sequence composed of several regions of distinct function for
coding the synthesis of RNA or polypeptide.
There are coding and non coding regions in the DNA associated with genes:
The non coding regions include controlling regions (promoters and transcriptional
regulatory sequences), introns and polyadenylation signals.
Coding regions (open reading frame) include exons sequences to be translated.
Controlling regions determine the pattern of expression of a particular gene in a
particular cell type. Specifically, the promoter dictates where transcription starts
and is located just upstream of that site. Enhancers influence the level of
transcription as well as the cell-type specificity. Enhancers can be located at
varying distances and upstream, within, or downstream, of the genes they control.
The portions of the gene that encode the amino acid sequence of a protein are
called the exons. These protein-coding regions can be interrupted by intervening
sequences, or introns. Introns can vary in number from 0 to as many as 80 per
gene.
Fig.14. Eukaryotic gene structure.
II. DNA sequences of eukaryotic protein-coding gene
1) The usual linear order for DNA sequences at a gene is:
a) Regulatory element(s) (where activators or suppressors bind);
b) promoter region (where the RNA polymerase complex binds);
c) transcription start site (in 5' UTR);
d) exon(s);
e) introns (between exons, 5'GT and 3'AG, variable number);
f) 3' UTR consisting of a translation stop codon (TAA, TGA, or TAG);
g) AATAAA polyadenylation signal; and the site for addition of poly A tail.
DNA sequences of gene
Feature
Description
Promoters
TATA-box (-25); many genes have a GC rich region
upstream of (and often including) the first exon.
Unlike the rest of the genome, it has no deficit of the
dinucleotide CpG.
Exons
These are the parts of the gene which will remain in the
mRNA after the primary transcript is processed.
Introns
These parts of the gene which are removed from the
primary transcripts by splicing
translated
region
This is the region of the gene which codes for protein
(exons).
5'UTR
The region of exon 1 between the cap site and the start of
translation at the first AUG codon.
3'UTR
The region of the final exon between the translation stop
codon and the polyA addition site at the end of the
transcript.
2) Enhancers
Some transcription factors ("Enhancer-binding protein") bind to regions of DNA
that are thousands of base pairs away from the gene they control. They are named
Enhancers.
Enhancers can be located upstream, downstream, or even within the gene they
control. Binding the transcription factors with enhancer increases the rate of
transcription of the gene.
Enhancer-binding proteins have sites that bind to transcription factors ("TF")
assembled at the promoter of the gene. This would draw the DNA into a loop:
3) Silencers
Silencers are control regions of DNA that may be located thousands of base pairs
away from the gene they control. However, when transcription factors bind to
them, expression of the gene they control is repressed.
4) Hormones exert many of their effects by forming transcription factors
The complexes of hormones with their receptor represent one class of transcription
factor. Hormone "response elements", to which the complex binds, are promoter
sites.
Embryonic development requires the coordinated production and distribution of
transcription factors.
5) Insulators are


stretches of DNA (as few as 42 base pairs)
located between the
o enhancer(s) and promoter or
o silencer(s) and promoter of adjacent genes
o The insulator prevents a gene from being influenced by the activation
(or repression) of its neighbors.
There is an insulator between the alpha gene promoter and the delta gene promoter
that ensures that activation of one does not spread over to the other.
Fig. 15. The enhancer for the promoter of the gene for the delta chain of the
gamma/delta T-cell receptor for antigen (TCR) is located close to the promoter
for the alpha chain of the alpha/beta TCR (on chromosome 14 in humans). There
is an insulator between the alpha gene promoter (Pα) and the delta gene promoter
(Pδ). T - cell must choose between one or the other.
All insulators discovered so far in vertebrates work only when bound by a protein
designated CTCF ("CCCTC binding factor"; named for a nucleotide sequence
found in all insulators). CTCF has 11 zinc fingers.
III. Other mechanisms for regulation of eukaryotic gene expression
1) Methylation. Example: In mammals (mice, humans, pigs), only the allele for
insulin-like growth factor-2 (IGF2) inherited from one's father is active; that
inherited from the mother is not — a phenomenon called imprinting.
The mechanism: the mother's allele has an insulator between the IGF2 promoter
and enhancer. So does the father's allele, but in his case, the insulator has been
methylated. CTCF can no longer bind to the insulator, and so the enhancer is now
free to turn on the father's IGF2 promoter.
2) Alternative Splicing is exon skipping and splicing of mRNA to make more than
one protein from a single gene. Some genes have alternate splice sites so that
several different proteins can be produced from the multiple mRNAs that are
produced from the same gene. The ability to make more than one gene product
(polypeptide) from a single gene explains in part how we can have many more
gene products than only the number of genes sequenced in the Human Genome
project.
3) Post transcriptional processes that modify the initial RNA transcript usually
include 5' cap addition, 3' poly A addition, and alternative splicing of introns to
form different mRNAs from the same gene. The use of alternative promoters is
common and is used to generate cell type specific mRNAs. These alternative
promoters may be found within introns of the gene. The human dystrophin (DMD)
gene which has more than 79 exons has at least eight different alternative
promoters.
4) Post translational cleavage of proteins, while rare, can also occur as in the case
of insulin and some hormones.
Many different genes and many different types of cells share the same transcription
factors — not only those that bind at the basal promoter but even some of those
that bind upstream. The unique combination of promoter sites and the transcription
factors that are chosen is the main type of regulation of eukaryotic genes.