Control of
Eukaryotic Genes
AP Biology
2007-2008
The BIG Questions…
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How are genes turned on & off
in eukaryotes?
How do cells with the same genes
differentiate to perform completely
different, specialized functions?
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Development: cellular level
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Cell division
Differentiation
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cells become specialized in structure & function
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if each kind of cell has the same genes,
how can they be so different
shutting off of genes = loss of totipotency
Morphogenesis
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“creation of form” = give organism shape
basic body plan
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polarity
 one end is different than the other
symmetry
 left & right side of body mirror each other
asymmetry
 pssst, look at your hand…
Development: step-by-step
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Gamete formation
Fertilization
Cleavage (cell division, mitosis)
Gastrulation (morphogensis)
Organ formation (differentiation)
Growth & tissue formation
(differentiation)
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Evolution of gene regulation
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Prokaryotes
single-celled
 evolved to grow & divide rapidly
 must respond quickly to changes in
external environment
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exploit transient resources
Gene regulation
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turn genes on & off rapidly
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flexibility & reversibility
adjust levels of enzymes
for synthesis & digestion
Cell signaling
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Regulating the expression of genes that
affect the developmental fate of the cell
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Gastrulation
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zygote  blastula  gastrula
How you looked
as a blastula…
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Gastrulation
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Cells change size & shape: sheets of cells
expand & fold inward & outward
Changes in cell
shape involve
reorganization
of cytoskeleton
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Stem cells
pluripotent cells
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Evolution of gene regulation
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Eukaryotes
multicellular
 evolved to maintain constant internal
conditions while facing changing
external conditions
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homeostasis
regulate body as a whole
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growth & development
 long term processes
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specialization
 turn on & off large number of genes
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must coordinate the body as a whole rather
than serve the needs of individual cells
Master control genes
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Homeotic genes
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master regulatory
genes
in flies these genes
identify body
segments & then
turn on other
appropriate genes
to control further
development of
those body sections
Homeotic genes
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Mutations to homeotic genes produce flies
with such strange traits as legs growing from
the head in place of antennae.
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structures characteristic of a particular part of
the animal arise in wrong place
antennapedia flies
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Homeobox DNA
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Master control
genes evolved
early
Conserved for
hundreds of
millions of years
Homologous
homeobox genes in
fruit flies &
vertebrates
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kept their
chromosomal
arrangement
Evolutionary Constraints on
Development
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Basic body plans of the major animal
groups have not changed due to a limited
number of homeotic genes (master
genes)
These genes have imposed limits
taxonomic / evolutionary
 physical
 architectural
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Points of control
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The control of gene
expression can occur at any
step in the pathway from
gene to functional protein
1. packing/unpacking DNA
2. transcription
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation
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1. DNA packing
How do you fit all
that DNA into
nucleus?
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DNA coiling &
folding
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double helix
nucleosomes
chromatin fiber
looped
domains
chromosome
from DNA double helix to
AP Biology chromosome
condensed
Nucleosomes
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8 histone
molecules
“Beads on a string”
1st level of DNA packing
 histone proteins
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8 protein molecules
positively charged amino acids
bind tightly to negatively charged DNA
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DNA
packing movie
DNA packing as gene control
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Degree of packing of DNA regulates transcription
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tightly wrapped around histones
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no transcription
genes turned off
 heterochromatin
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
H
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E
DNA methylation
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Methylation of DNA blocks transcription factors
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no transcription
 genes turned off
attachment of methyl groups (–CH3) to cytosine
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nearly permanent inactivation of genes
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C = cytosine
ex. inactivated mammalian X chromosome = Barr body
Histone acetylation
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Acetylation of histones unwinds DNA
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loosely wrapped around histones
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attachment of acetyl groups (–COCH3) to histones
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enables transcription
genes turned on
conformational change in histone proteins
transcription factors have easier access to genes
2. Transcription initiation
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Control regions on DNA
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promoter
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nearby control sequence on DNA
binding of RNA polymerase & transcription
factors
“base” rate of transcription
enhancer
distant control
sequences on DNA
 binding of activator
proteins
 “enhanced” rate (high level)
of transcription
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Control of transcription movie
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Model for Enhancer action
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Enhancer DNA sequences
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Activator proteins
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distant control sequences
bind to enhancer sequence
& stimulates transcription
Silencer proteins
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bind to enhancer sequence
& block gene transcription
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Turning
on Gene movie
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
A
E
F
B
TFIID
RNA polymerase II
H
Core promoter
and initiation complex
Initiation Complex at Promoter Site binding site of RNA polymerase
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3. Post-transcriptional control
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Alternative RNA splicing
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variable processing of exons creates a
family of proteins
4. Regulation of mRNA degradation
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Life span of mRNA determines amount
of protein synthesis
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mRNA can last from hours to weeks
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RNA
processing movie
RNA interference
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Small interfering RNAs (siRNA)
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short segments of RNA (21-28 bases)
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bind to mRNA
create sections of double-stranded mRNA
“death” tag for mRNA
 triggers degradation of mRNA
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cause gene “silencing”
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post-transcriptional control
turns off gene = no protein produced
siRNA
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Action of siRNA
dicer
enzyme
mRNA for translation
siRNA
double-stranded
miRNA + siRNA
breakdown
enzyme
(RISC)
mRNA degraded
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functionally
turns gene off
RNA interference
RNAi
http://www.pbs.org/wgbh/nov
a/body/rnai.html
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Andrew Fire
Stanford
Craig Mello
U Mass
1990s | 2006
“for their discovery of
RNA interference —
gene silencing by
double-stranded RNA”
5. Control of translation
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Block initiation of translation stage
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regulatory proteins attach to 5' end of mRNA
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prevent attachment of ribosomal subunits &
initiator tRNA
block translation of mRNA to protein
Control of Translation
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http://www.hhmi.org/biointeractive/tran
slation-advanced-detail
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6-7. Protein processing & degradation
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Protein processing
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folding, cleaving, adding sugar groups,
targeting for transport
Protein degradation
ubiquitin tagging
 proteasome degradation
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Protein
processing movie
1980s | 2004
Ubiquitin
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“Death tag”
mark unwanted proteins with a label
 76 amino acid polypeptide, ubiquitin
 labeled proteins are broken down
rapidly in "waste disposers"
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AP
proteasomes
Aaron Ciechanover
Biology Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Proteasome
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Protein-degrading “machine”
cell’s waste disposer
 breaks down any proteins
into 7-9 amino acid fragments
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cellular recycling
6
7
Gene Regulation
protein
processing &
degradation
1 & 2. transcription
- DNA packing
- transcription factors
5
4
initiation of
translation
mRNA
processing
3 & 4. post-transcription
- mRNA processing
- splicing
- 5’ cap & poly-A tail
- breakdown by siRNA
5. translation
- block start of
translation
1 2
initiation of
transcription
AP Biology mRNA splicing
3
6 & 7. post-translation
- protein processing
- protein degradation
4
mRNA
protection
Epigenetics
For more than a decade, scientists
have had access to a reference
human genome. Now, the
equivalent for the epigenome has
been published, in a collection of
papers appearing on 18 February
in Nature and several other
journals.
AP Biology
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Researchers looked for features including chemical tweaks to
DNA that prime genes to be switched on or off, and alterations
to the 'histone' proteins around which DNA is wrapped.
Chemical or structural modifications to histones can affect which
genes the cellular machinery translates into proteins and which
remain silent. Such epigenetic changes can dramatically affect a
cell’s behaviour and function.
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The epigenomes also contain hints of how epigenetic changes
could be involved in diseases, including cancer, Alzheimer's
disease and autoimmune diseases.
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Taken together, the work demonstrates how a cell’s epigenome
is complex and exquisitely arranged — just like a Beethoven
symphony.
AP Biology
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Epigenome The Symphony in Your
Cells
Nature Video

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http://www.nature.com/news/epigenome
-the-symphony-in-your-cells-1.16955
Gene Control in Eukaryotes
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X-Inactivation
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X-inactivation
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Female mammals inherit 2 X chromosomes
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one X becomes inactivated during
embryonic development
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condenses into compact object = Barr body
which X becomes Barr body is random
 patchwork trait = “mosaic”
patches of black
XH 
XH Xh
tricolor cats
can only be
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female
Xh
patches of orange
Turn your
Question Genes on!
AP Biology
2007-2008
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Gene Regulation in Eukaryotes
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http://www.hhmi.org/biointeractive/regul
ation-eukaryotic-dna-transcription
6
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Gene Regulation
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3 & 4. _________________
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5. _________________
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6 & 7. _________________
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Kim Foglia
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As always a huge thank you to Kim for
her most most most excellent work
AP Biology