2012NSC Molecular Biology

Module 2
Eukaryotic gene expression

Snustad 7th Ed – Chapter 18

Pierce 6th Ed – Chapter 17
Regulating Eukaryotic Gene
Expression: An Overview

Primarily in Eukaryotes

Prokaryotes and Eukaryotes

Primarily in Eukaryotes

Prokaryotes and Eukaryotes

Prokaryotes and Eukaryotes

Level of Gene
Control

Alteration of structure
 Chromatin organisation
• Chromatin is a
complex of DNA and
proteins
• Most abundant
protein are histones.
– Contain high % of
arginine and lysine
(positively charged)

• Nucleosome is the core particle consisting of DNA

wrapped around eight histone proteins
– Each of these histone proteins has a flexible ‘tail’ (11-37 amino
acids) which extend out from the nucleosome.
• Histone H1 acts as a clamp
Euchromatin and Heterochromatin
• Variation of density of chromatin gives
banding pattern to stained chromosomes

• Dark stain: heterochromatin

– Centromeres
– Telomeres
– Interspersed
• Light stain: euchromatin
– Vast majority of eukaryotic genes are located in
euchromatin
 The Drosophila wm4 Allele
• The white gene encodes for red eyes.

• The wm4 allele is an inversion that relocates the

white gene to a heterochromatic region.

• Position-effect variegation occurs in wm4 mutants.

euchromatin White heterochromatin

white

White
euchromatin heterochromatin

Fig 20.16 Snustad and Simmons 5th Ed.

 Transcription in Lampbrush
Chromosome Loops
• Chromatin must be “open” to
the transcriptional apparatus
for transcription to occur.

• The lateral loops in

Fig 20.13 Snustad and Simmons 5th Ed.
Meiotic chromosomes of amphibian oocytes.
lampbrush chromosomes are
regions of intense
transcriptional activity; the
condensed axes are relatively
inactive for transcription.
 Transcription in Drosophila
Polytene Chromosome Puffs
• Chromomeres (bands)
expand into diffuse puffs
during the course of
development.
• The puffs contain genes
that are actively
transcribed.
• Diffuse, expanded
chromosomal regions are
sites of intense RNA
synthesis.
Fig 11.6 Pierce 6th Ed.
Modification of chromatin structure:
Chromatin Remodelling
• Chromatin-remodelling
complexes alter
chromatin structure
without altering the
chemical structure of
histones.
– Example SWI/SNF complex
• Reposition nucleosomes
so that the transcription
machinery can bind to the
necessary promoter.
Histone modification
Acetylation
• Acetyltransferases (HATs)
add acetyl groups (CH3CO)
to lysine on the histone tails
• Stimulates transcription by
destabilising the chromatin
structure
– open configuration

Deacetylation
• Deacetylases (HDACs) strip
acetyl groups from histones

https://www.youtube.com/watch?v=rtrjhvaMTAE (4 mins)
Example: Flowering in Arabidopsis.
The SV40 Enhancer Region is
Nucleosome-Free
 Silencing of vsg Genes in
Trypanosomes

Fig 20.18 Snustad and Simmons 5th Ed.

• There are numerous Variant Surface Glycoprotein

(vsg) genes, but only one is expressed.

• The expressed gene lies in an Expression Site (ES)

controlled by a promoter 40 to 50 kb away.
vsg Replacement Through
Insertional Copying

Fig 20.18 Snustad and Simmons 5th Ed.

vsg Replacement Through
Crossing-over

Fig 20.18 Snustad and Simmons 5th Ed.

 DNA Methylation
• Most methylated cytosines
are found in the dinucleotide
sequence CG, denoted
mCpG.
• DNA methylation is catalysed
by a family of enzymes called
DNA methyltransferases
(DNMT#)
m
5’ – CG – 3’ • Methylated gene promoters
3’ – GC – 5’
m
are less likely to be
transcribed than
unmethylated promoters.
 How to make a Queen Bee
• Queen and worker Bees have the same
genetic background
• Differ in diet
• Royal Jelly suppresses Dnmt3
• Queen characteristics are expressed
• Large size, ovaries

EPIGENETICS
 DNA Methylation function

• Methyl group of mCpG sits in

major groove
• mCpG attracts regulatory proteins
which repress transcription
• mCpG attracts histone
deacetylase enzymes
 CpG Islands
• CpG dinucleotides occur less often than
expected in mammalian genomes
• probably due to mutation into TpG dinucleotides over
the course of evolution.

• The distribution of CpG dinucleotides is uneven.

• CpG-rich segments (1-2kb long) are called CpG
islands.

• Most CpG islands are located near transcription

start sites; cytosines in these regions are rarely
methylated.
 CpG Islands
• Most CpG
islands are
located near
transcription
start sites

• Useful for
identifying
genes
 Methylated DNA is Associated
with Transcriptional Repression
• The inactive X chromosome in female
mammals is extensively methylated.
• Regions of mammalian genomes containing
repetitive sequences are methylated.
• Proteins that repress transcription have been
shown to bind to methylated DNA.
• DNA methylation in mammals is responsible
for imprinting, in which the expression of a
gene is controlled by its parental origin.
 Imprinting of the Mouse Igf2 Gene

Figure 18.13 Snustad and Simmons

Pierce 6th Ed.: Chapter 5 (pg 131) Chapter 21 (pg 655)

Paternally donated chromosome
 Concept Check

Which alterations must have occurred for an

eukaryotic promoter to be exposed to the
transcription machinery?
 Gene Amplification
• Gene amplification: an increase in the
number of copies of a gene without a
proportional increase in other genes.

• Example: In amphibian oocytes, the 5.8S,

18S, and 28S rRNA genes are amplified by
the creation of extrachromosomal copies of
the genes to allow increased gene
expression. The 5S rRNA genes are present
in thousands of copies on the chromosomes.
 Summary: Alteration of
structure effects transcription

• Transcription occurs preferentially in loosely

organized chromosome regions exemplified
by the loops of lampbrush chromosomes and
the puffs of polytene chromosomes.

• During transcriptional activation, chromatin is

remodeled by multiprotein complexes.
• With or without altering the structure of histones
 Summary
• In trypanosomes, only one telomeric variant
surface glycoprotein (vsg) gene is expressed;
all other vsg genes, including those at
telomeres, are silent.
• Methylation of DNA is associated with gene
silencing in mammals.
• The expression of a gene that is imprinted is
conditioned by the gene’s parental origin.
• Increased gene expression may be achieved
by amplifying the DNA, either within
chromosomes or on extrachromosomal DNA
molecules.