Control of
Eukaryotic Genes
(Ch. 19)
The BIG Questions…
• How are genes turned
on & off
in eukaryotes?
• How do cells with the
same genes
differentiate to perform
completely different,
specialized functions?
Evolution of gene regulation
• Prokaryotes
– single-celled
– evolved to grow & divide rapidly
– must respond quickly to changes in external
environment
• exploit transient resources
• Gene regulation- Operons
– turn genes on & off rapidly
• flexibility & reversibility
– adjust levels of enzymes
for synthesis & digestion
Evolution of gene
regulation
• Eukaryotes
– multicellular
– evolved to maintain homeostasis
– regulate body as a whole
• specialization
–turn on & off large number of genes
• must coordinate the body as a whole
rather than serve the needs of individual
cells
Points of control
• The control of gene
expression can occur at any
step in the pathway from
gene to functional protein
1. DNA packing
from DNA double helix to
condensed chromosome
Nucleosomes
• “Beads on a string”
– 1st level of DNA packing
– histone proteins
• 8 protein molecules
• positively charged amino acids
• bind tightly to negatively charged DNA
8 histone
molecules
DNA packing as gene control
• Degree of packing of DNA regulates transcription
– tightly wrapped around histones
• no transcription
• genes turned off
 heterochromatin
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
DNA methylation
• Methylation of DNA blocks transcription factors
– attachment of methyl groups (–CH3) to cytosine
– nearly permanent inactivation of genes
• ex. inactivated mammalian X chromosome = Barr
body
Histone acetylation
Chromatin changes


Acetylation of histones
unwinds DNA
Loose histone wrapping




RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Histone
tails
enables transcription
genes turned on
attachment of acetyl groups
(–COCH3) to histones

Transcription
conformational change in
histone proteins
transcription factors
have easier access to
genes
DNA
double helix
Amino acids
available
for chemical
modification
(a) Histone tails protrude outward from a nucleosome
Unacetylated histones
Acetylated histones
(b) Acetylation of histone tails promotes loose chromatin
structure that permits transcription
2. Transcription initiation
• Control regions on DNA
– promoter
• nearby control sequence on DNA
• binding of RNA polymerase & transcription
factors
– enhancer
• distant control
sequences on DNA
• binding of activator
proteins
Model for Enhancer action
• Enhancer DNA sequences
– distant control sequences
• Activator proteins
– bind to enhancer sequence &
stimulates transcription
• Silencer proteins
– bind to enhancer sequence &
block gene transcription
Transcription complex
Activator Proteins
• regulatory proteins bind to DNA at
Enhancer Sites
distant enhancer sites
• increase the rate of transcription
regulatory sites on DNA
distant from gene
Enhancer
Activator
Activator
Activator
Coactivator
B
A
TFIID
E
F
RNA polymerase II
H
Core promoter
and initiation complex
Initiation Complex at Promoter Site binding site of RNA polymerase
Many control
elements for different
genes are the same
It is the combination
of control elements
that provides
specificity
14
3. Post-transcriptional control
• Alternative RNA splicing
– variable processing of exons creates a
family of proteins
4. Regulation of mRNA
degradation
• Life span of mRNA determines amount of
protein synthesis
– mRNA can last from hours to weeks
RNA interference
1 The microRNA (miRNA)
precursor folds
back on itself,
held together
by hydrogen
bonds.
22 An enzyme
called Dicer moves
along the doublestranded RNA,
cutting it into
shorter segments.
3 One strand of
each short doublestranded RNA is
degraded; the other
strand (miRNA) then
associates with a
complex of proteins.
4 The bound
miRNA can base-pair
with any target
mRNA that contains
the complementary
sequence.
5 The miRNA-protein
complex prevents gene
expression either by
degrading the target
mRNA or by blocking
its translation.
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Protein
complex
Dicer
Degradation of mRNA
OR
miRNA
Target mRNA
Hydrogen
bond
Blockage of translation
A Brief, RNAi Cartoon
miRNA’s
• Scientists discovery video
• Animation of miRNA function
19
RNA interference
1990s | 2006
“for their discovery of
RNA interference —
gene silencing by
double-stranded RNA”
Andrew Fire
Stanford
Craig Mello
U Mass
5. Control of translation
• Block initiation of translation stage
– regulatory proteins attach to 5' end of mRNA
• prevent attachment of ribosomal subunits &
initiator tRNA
• block translation of mRNA to protein
6-7. Protein processing & degradation
• Protein processing
– folding, cleaving, adding sugar groups, targeting
for transport
• Protein degradation
– ubiquitin tagging
– proteasome degradation
Ubiquitin
1980s | 2004
• “Death tag”
– mark unwanted proteins with a label
– 76 amino acid polypeptide, ubiquitin
– labeled proteins are broken down rapidly in
"waste disposers"
• proteasomes
Aaron Ciechanover
Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Proteasome
• Protein-degrading “machine”
– cell’s waste disposer
– breaks down any proteins
into 7-9 amino acid fragments
• cellular recycling
6
7
Gene Regulation
protein
processing &
degradation
1 & 2. transcription
- DNA packing
- transcription factors
3 & 4. post-transcription
- mRNA processing
- splicing
4
- 5’ cap & poly-A tail
mRNA
- breakdown by siRNA
processing
5
initiation of
translation
5. translation
- block start of
translation
1 2
initiation of
transcription
3
mRNA splicing
6 & 7. post-translation
- protein processing
- protein degradation
4
mRNA
protection
Concept Check
1. Do miRNA’s increase or decrease gene
expression?
2. Does histone de-acetylation increase or
decrease gene expression?
26
Genome Sizes and Estimated Numbers of Genes*
Types of DNA sequences in the
human genome
Exons (regions of genes coding
for protein, rRNA, tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Introns and
regulatory
sequences
(24%)
Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Large-segment
duplications (5–6%)
Unique
noncoding
DNA (15%)
Just how little of out Genome Codes for
Genes?
QuickTime™ and a
H.264 decompressor
are needed to see this picture.
Cancer results from genetic
changes in cell cycle control
30
Proto-oncogene --> oncogene
31
32
Multistep Model
of cancer
33
Genome Evolution
• How did our genome get so big?
34
35
36
• The similarity in the amino acid sequences of the
various globin proteins
– Supports this model of gene duplication and mutation
Table 19.1
37
Evolution of Genes with
Novel Functions
• The copies of some duplicated genes
– Have diverged so much during evolutionary
time that the functions of their encoded
proteins are now substantially different
38
39
Concept check
1. How much of the human genome consists of
exons?
2. How can exon shuffling lead to the evolution
of a new gene
40
Turn your
Question Genes on!
A larger portion of the DNA in a eukaryotic cell is
transcribed than would be predicted by the proteins
made by the cell. What is being transcribed and what is
its function?
1.
Multiple enhancer regions are being transcribed to amplify the
transcription of protein-coding genes.
2.
These transcriptions are of non-coding “junk” DNA that is a
remnant of mutated protein coding segments. The transcripts
are degraded by nuclear enzymes.
3.
The additional DNA that is transcribed is introns that are
excised fro the primary transcript in the produciton of mRNA.
4.
Many RNA coding genes are transcribed. Precursor RNAs
fold into hairpin structures, which are cut and processed into
miRNAs that regulate translation of mRNAs.
42
How is the coordinated transcription of genes involved in
the same pathway regulated?
1.
The genes are transcribed in one transcription unit, although
each gene has its own promoter.
2.
The genes are located in the same region of the chromosome,
and enzymes de-acetylate the entire region so that
transcription may begin.
3.
A steroid hormone selectively binds to the promoters for all the
genes.
4.
The genes have the same combination of control elements in
the enhancer that bind with the particular activators present in
the cell.
43
Histones are
1.
Small positively charged proteins that bind tightly to DNA
2.
Small bodies in the nucleus involved in rRNA synthesis
3.
Basic units of DNA packing consisting of DNA wound around a
protein core.
4.
DNA bending proteins that facilitate formation of transcription
initiation complexes.
5.
Proteins responsible for producing repeating sequences at
telomeres.
44
Heterochromatin
1.
Has a higher degree of packing than does euchromatin.
2.
Is visible with a light microscope during interphase.
3.
Is not actively involved in transcription
4.
Makes up metaphase chromosomes
5.
Is all of the above.
45
What is the main reason that prokaryotic genes average
1,000 nucleotride base pairs whereas human genes
average about 27.000 base pairs?
1.
Prokaryotes have smaller, bue many more individual genes.
2.
Prokaryotes are more ancient organisms, longer genes arose
later in evolution.
3.
Prokaryotes are much simpler organism humans have many
types of differentiated cells.
4.
Prokaryotic genes do not have introns, human genes have
many
5.
Human proteins are much larger and more complex than
prokaryotic proteins.
46
A eukaryotic gene typically has all of the following
associated with it except
1.
A promoter
2.
An operator
3.
Enhancers
4.
Introns and exons
5.
Control elements.
47