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Genetics: Analysis and Principles
Robert J. Brooker
CHAPTER 15
GENE REGULATION IN
EUKARYOTES
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INTRODUCTION
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Eukaryotic organisms have many benefits from
regulating their genes
For example
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They can respond to changes in nutrient availability
They can respond to environmental stresses
In plants and animals, multicellularity and a more
complex cell structure, also demand a much greater
level of gene expression
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INTRODUCTION
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Gene regulation is necessary to ensure
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1. Expression of genes in an accurate pattern during the
various developmental stages of the life cycle
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Some genes are only expressed during embryonic stages,
whereas others are only expressed in the adult
2. Differences among distinct cell types

Nerve and muscle cells look so different because of gene
regulation rather than differences in DNA content
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Figure 15.1
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15.1 REGULATORY
TRANSCRIPTION FACTORS
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Transcription factors are proteins that influence the
ability of RNA polymerase to transcribe a given gene
There are two main types
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General transcription factors
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Required for the binding of the RNA pol to the core promoter and
its progression to the elongation stage
Are necessary for basal transcription
Regulatory transcription factors
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Serve to regulate the rate of transcription of nearby genes
They influence the ability of RNA pol to begin transcription of a
particular gene
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Regulatory transcription factors recognize cis
regulatory elements located near the core promoter
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These sequences are known as response elements,
control elements or regulatory elements
The binding of these proteins to these elements,
affects the transcription of an associated gene
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A regulatory protein that increases the rate of
transcription is termed an activator
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A regulatory protein that decreases the rate of
transcription is termed a repressor
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The sequence it binds is called an enhancer
The sequence it binds is called a silencer
Refer to Figure 15.2
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Functional Domains of Eukaryotic
Transcription Factors
• DNA binding domain – DBD
– Binds specific sequence of base pairs
• Transcriptional activation domain – TAD
– Interacts with basal txn factors or directly with RNA
polymerase II
• Protein-protein interaction domain – PPID
– Homo- & Hetero dimerization domains
– Interaction with other txn factors (besides the basal
apparatus)
Transcription Factor Families
Family
Homeodomain
Representative
Hox
Hoxa-1, Antp, eve, en
POU
Pit-1,Unc-86, Oct-2, Brn-5
LIM
Paired Box
Lim-1, Isl-1
Pax-1,2,6, Prd
Forkhead/Winged Helix
Fkh, HNF-3
Basic
leucine-zipper
helix-loop-helix
AP1, Myc, C/EBP
MyoD, Ac, da, emc
Zinc-finger
monomeric
WT-1, Krox-20, Kr, hb
steroid receptors
GR, ER, RAR, kni
Sox
Sry, SoxD, Sox2
MADS box
MEF-1, MCM-1, AG, DEF, SRF
Structural Features of Regulatory
Transcription Factors
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Transcription factor proteins contain regions, called
domains, that have specific functions
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One domain could be for DNA-binding
Another could provide a binding site for effector molecules
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A motif is a domain or portion of it that has a very
similar structure in many different proteins
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Figure 15.3 depicts several different domain
structures found in transcription factor proteins
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Composed of one -helix and
two b-sheets held together by
a zinc (Zn++) metal ion
Figure 15.3
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Zinc Finger DNA Binding Domain
Zinc Finger DNA Binding Domains
Interacting with DNA
Protein-DNA Contacts of Zif268
Specificity of Amino Acids for DNA Site
Recognition
Steroid Hormone Receptor Dimers Binding DNA
Helix-Turn-Helix
DNA Binding
Motif
The
Homeodomain
Hydrogen bonding between an -helix and nucleotide
bases is one way a transcription factor can bind to DNA
Figure 15.3
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Helix-turn-Helix
Motif Found in l
Repressor
Homeodomain First Identified in Genes Causing
Homeotic Transformations
Antennapedia
Ultrabithorax
Note: Helix-loop-helix motifs can
also mediate protein dimerization
Figure 15.3
Basic Domain Coupled with Helix-loopHelix (bHLH)
Leucine Zipper and bZip domains
Two -helices intertwined
due to leucine motifs
Homodimers are formed by two
identical transcription factors;
Heterodimers are formed by two
different transcription factors
Figure 15.3
Alternating leucine residues in
both proteins interact (“zip up”),
resulting in protein dimerization
Basic Domain Coupled with Leucine Zipper
(bZip)
Types of Activation Domains
Another activation domain is a
S/T rich sequence
Chimeric Transcription Factors
Demonstrate Independent Domain
Functions
Figure 15.2
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Mediation of TFIID binding
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Transcriptional activator recruits TFIID
to the core promoter and/or activates its
function
Thus, transcription will be activated
Activator
protein
Enhancer

ON
Coactivator
TFIID
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Coding sequence
Core
promoter
The activator/coactivator complex recruits TFIID to the core promoter
and/or activates its function. Transcription will be activated.
Transcriptional repressor inhibits TFIID
binding to the core promoter or inhibits
its function
Thus, transcription will be repressed
Regulation of Transcription Factors
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Binding of an
effector molecule
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Protein-protein
interactions
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Covalent
modification
Heat shock protein
Heat shock proteins
leave when hormone
binds to receptor
Steroid Hormone
Receptors
Formation of a
homodimer
Nuclear localization
Sequence is exposed
Glucocorticoid
Response Elements
These function as
enhancers
Transcription of target
gene is activated
Figure 15.6
The CREB Protein
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The CREB protein is another regulatory
transcriptional factor functioning within living cells
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CREB is an acronym for cAMP response element-binding
CREB protein becomes activated in response to cellsignaling molecules that cause an increase in cAMP
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Cyclic adenosine monophosphate
The CREB protein recognizes a response element with the
consensus sequence 5’–TGACGTCA–3’

This has been termed a cAMP response element (CRE)
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Regulation by phosphorylation CREB
Could be a hormone,
neurotransmitter,
growth factor, etc.
Acts as a
second
messenger
Activates
protein
kinase A
Phosphorylated CREB
binds to DNA and
stimulates transcription
Unphosphorylated CREB
can bind to DNA, but
cannot activate RNA pol
Positioned at regular intervals from -3,000 to + 1,500
Disruption in nucleosome positioning
from -500 to + 200
Figure 15.3
Changes in nucleosome position during the activation of the b-globin gene
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Chromatin Remodeling
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As discussed in Chapter 12, there are two common
ways in which chromatin structure is altered
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1. Covalent modification of histones
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2. ATP-dependent chromatin remodeling
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1. Covalent modification of histones
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Amino terminals of histones are modified in various ways
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Acetylation; phosphorylation; methylation
Adds acetyl groups, thereby
loosening the interaction
between histones and DNA
Figure 12.13
Removes acetyl groups,
thereby restoring a
tighter interaction
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2. ATP-dependent chromatin remodeling
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The energy of ATP is used to alter the structure of
nucleosomes and thus make the DNA more accessible
Proteins are members of the
SWI/SNF family
Mutants in SWI are defective in
mating type switching
Mutants in SNF are
sucrose non-fermenters
Figure 12.13
These effects may significantly alter
gene expression
DNA Methylation
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DNA methylation is a change in chromatin structure
that silences gene expression
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It is common in some eukaryotic species, but not all
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Yeast and Drosophila have little DNA methylation
Vertebrates and plants have abundant DNA methylation
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In mammals, ~ 2 to 7% of the DNA is methylated
(or DNA methylase)
CH3
Only one strand is
methylated
CH3
Both strands are
methylated
CH3
Figure 15.15
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DNA methylation usually inhibits the transcription of
eukaryotic genes
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Especially when it occurs in the vicinity of the promoter
In vertebrates and plants, many genes contain
CpG islands near their promoters
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These CpG islands are 1,000 to 2,000 nucleotides long
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In housekeeping genes
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The CpG islands are unmethylated
Genes tend to be expressed in most cell types
In tissue-specific genes
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The expression of these genes may be silenced by the
methylation of CpG islands
Transcriptional
activator binds to
unmethylated DNA
This would inhibit the
initiation of transcription
Figure 15.16 Transcriptional silencing via methylation
Figure 15.16 Transcriptional silencing via methylation
DNA Methylation is Heritable

Methylated DNA sequences are inherited during
cell division
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