Regulation of Gene Expression

1
Regulation of Gene Expression
2
16 Regulation of Gene Expression

• 16.1 How Is Gene Expression Regulated in
  Prokaryotes?
• 16.2 How Is Eukaryotic Gene Transcription
  Regulated?
• 16.3 How Do Viruses Regulate Their Gene
  Expression?
• 16.4 How Do Epigenetic Changes Regulate Gene
  Expression?
• 16.5 How Is Eukaryotic Gene Expression Regulated
  After Transcription?

3
16 Regulation of Gene Expression

• Behavioral epigenetics study of heritable
  changes in gene expression that do not involve
  changes in the DNA sequence.
• Methylation of some gene promoters may result
  from high levels of stress, and inhibit gene
  transcription. Methylation in the glucocorticoid
  receptor gene may result in behavioral problems.

Opening Question Can epigenetic changes be
manipulated?
4
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Prokaryotes can make some proteins only when they
  are needed. To shut off supply of a protein, the
  cell can
• Downregulate mRNA transcription
• Hydrolyze mRNA, preventing translation
• Prevent mRNA translation at the ribosome
• Hydrolyze the protein after it is made
• Inhibit the proteins function

5
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• The earlier the cell can stop protein synthesis,
  the less energy is wasted.
• Blocking transcription is more efficient than
  transcribing the gene, translating the message,
  and then degrading or inhibiting the protein.

6
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Gene expression begins at the promoter.
• Two types of regulatory proteins can bind to
  promoters
• Negative regulationa repressor protein prevents
  transcription
• Positive regulationan activator protein
  stimulates transcription

7
Figure 16.1 Positive and Negative Regulation
8
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• E. coli in the human intestine must adjust
  quickly to changes in food supply.
• Glucose is the easiest sugar to metabolize.
• Lactose is ß-galactoside (disaccharide of
  galactose and glucose).

9
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Three proteins are need for the uptake and
  metabolism of lactose.
• ?-galactoside permeasecarrier protein that moves
  lactose into the cell
• ?-galactosidasehydrolyses lactose
• ?-galactoside transacetylasetransfers acetyl
  groups from acetyl CoA to certain ?-galactosides

10
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• If E.coli is grown with glucose but no lactose,
  no enzymes for lactose conversion are produced.
• If lactose is predominant and glucose is low,
  E.coli synthesizes all three enzymes after a
  short lag period.

11
Figure 16.2 An Inducer Stimulates the Expression
of a Gene for an Enzyme
12
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• During the lag period, mRNA for ß-galactosidase
  is produced.
• If lactose is removed, the mRNA level goes down.

13
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Compounds that stimulate protein synthesis are
  called inducers
• The proteins are inducible proteins.
• Constitutive proteins are made at a constant rate.

14
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Metabolic pathways can be regulated in two ways
• Allosteric regulation of enzyme-catalyzed
  reactions allows rapid fine-tuning
• Regulation of protein synthesis is slower but
  conserves energy and resources. Protein synthesis
  requires a lot of energy

15
Figure 16.3 Two Ways to Regulate a Metabolic
Pathway
16
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Structural genes specify primary protein
  structurethe amino acid sequence.
• The 3 structural genes for lactose enzymes are
  adjacent on the chromosome and share a promoter,
  forming the lac operon.

17
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• An operon is a gene cluster with a single
  promoter.
• A typical operon consists of
• A promoter
• Two or more structural genes
• An operatora short sequence between the promoter
  and the structural genes binds to regulatory
  proteins

18
Figure 16.4 The lac Operon of E. coli
19
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Three ways to control operon transcription
• An inducible operon regulated by a repressor
  protein
• A repressible operon regulated by a repressor
  protein
• An operon regulated by an activator protein

20
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• In the lac operon the operator can bind a
  repressor protein, which blocks transcription.
• The repressor has 2 binding sites one for the
  operator, and one for the inducer (lactose).
• When lactose is absent, the repressor prevents
  binding of RNA polymerase to the promoter.

21
Figure 16.5 The lac Operon An Inducible System
(Part 1)
22
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• When lactose is present, it binds to the
  repressor and changes the repressors shape.
• This prevents the repressor from binding to the
  operator, and then RNA polymerase can bind to the
  promoter, and the genes are transcribed.

23
Figure 16.5 The lac Operon An Inducible System
(Part 2)
24
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Other E. coli systems are repressiblethe operon
  is turned on unless repressed under specific
  conditions.
• In these systems, the repressor isnt bound to
  the operator until a co-repressor binds to it.
• The repressor then changes shape, binds to the
  operator, and blocks transcription.

25
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• The trp operon is a repressible system.
• The genes code for enzymes that catalyze
  synthesis of tryptophan.
• When there is enough tryptophan in the cell,
  tryptophan binds to the repressor, which then
  binds to the operator. Tryptophan is the
  co-repressor.

26
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Inducible systems metabolic substrate (inducer)
  interacts with a regulatory protein (repressor)
  repressor cant bind to operator and
  transcription proceeds.
• Repressible systems a metabolic product
  (co-repressor) binds to a regulatory protein,
  which then binds to the operator and blocks
  transcription.

27
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Inducible systems control catabolic pathwaysthey
  are turned on when substrate is available.
• Repressible systems control anabolic
  pathwaysthey are turned on until product
  concentration becomes excessive.

28
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Positive control an activator protein can
  increase transcription.
• If glucose and lactose levels are both high, the
  lac operon is not transcribed efficiently.
• Efficient transcription requires binding of an
  activator protein to its promoter.

29
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• If glucose levels are low, a signaling pathway
  leads to increased levels of cyclic AMP.
• cAMP binds to cAMP receptor protein (CRP)
  conformational change in CRP allows it to bind to
  the lac promoter.
• CRP is an activator of transcription its binding
  results in more efficient binding of RNA
  polymerase and thus increased transcription.

30
Figure 16.6 Catabolite Repression Regulates the
lac Operon
31
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• If glucose is abundant, CRP does not bind to the
  lac operon promoter and efficiency of
  transcription is reduced.
• This is catabolite repression, a system of gene
  regulation in which presence of a preferred
  energy source represses other catabolic pathways.

32
Figure 16.6 Catabolite Repression Regulates the
lac Operon
33
Table 16.1
34
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Promoters bind and orient RNA polymerase so that
  the correct DNA strand is transcribed.
• All promoters have consensus sequences that allow
  them to be recognized by RNA polymerase.
• Different classes of consensus sequences are
  recognized by regulatory proteins called sigma
  factors.

35
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Sigma factors bind to RNA polymerase and direct
  it to certain promoters.
• Genes for proteins with related functions may be
  at different locations in the genome, but share
  consensus sequences and can be recognized by
  sigma factors.

36
16.1 How Is Gene Expression Regulated in
Prokaryotes?

• Sigma-70 factor is active most of the time and
  binds to consensus sequences of housekeeping
  genes (genes normally expressed in actively
  growing cells).
• Others are activated only under specific
  conditions.

37
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• In development of multicellular organisms,
  certain proteins must be made at just the right
  times and in just the right cells.
• The expression of eukaryotic genes must be
  precisely regulated.
• Regulation can occur at several different points.

38
Figure 16.7 Potential Points for the Regulation
of Gene Expression (Part 1)
39
Figure 16.7 Potential Points for the Regulation
of Gene Expression (Part 2)
40
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Both prokaryotes and eukaryotes use DNA-protein
  interactions and negative and positive control to
  regulate gene expression.
• But there are differences, some dictated by the
  presence of a nucleus, which physically separates
  transcription and translation.

41
Table 16.2
42
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Eukaryote promoters contain a sequence called the
  TATA boxwhere DNA begins to denature.
• Promoters also include regulatory sequences
  recognized by transcription factors (regulatory
  proteins).

43
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• RNA polymerase II can only bind to the promoter
  after general transcription factors have
  assembled on the chromosome
• TFIID binds to TATA box then other factors bind
  to form an initiation complex.

44
Figure 16.8 The Initiation of Transcription in
Eukaryotes (Part 1)
45
Figure 16.8 The Initiation of Transcription in
Eukaryotes (Part 2)
46
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Some regulatory sequences are common to promoters
  of many genes, such as the TATA box.
• Some sequences are specific to a few genes and
  are recognized by transcription factors found
  only in certain tissues.
• These play an important role in cell
  differentiation.

47
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Enhancers regulatory sequences that bind
  transcription factors that activate transcription
  or increase rate of transcription.
• Silencers bind transcription factors that
  repress transcription.

48
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Most regulatory sequences are located near the
  transcription start site.
• Others may be located thousands of base pairs
  away. Transcription factors may interact with the
  RNA polymerase complex and cause the DNA to bend.
  

49
Figure 16.9 Transcription Factors and
Transcription Initiation
50
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Often there are many transcription factors
  involved.
• The combination of factors present determines the
  rate of transcription.
• Although the same genes are present in all cells,
  the fate of the cell is determined by which of
  its genes are expressed.

51
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Transcription factors have common structural
  motifs in the domains that bind to DNA.
• A common motif is helix-turn-helix

52
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• For DNA recognition, the structural motif must
• Fit into a major or minor groove
• Have amino acids that can project into interior
  of double helix
• Have amino acids that can bond with interior bases

53
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Many repressor proteins, such as the lac
  repressor, have helix-turn-helix motifs

54
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• During development, cell differentiation is often
  mediated by changes in gene expression.
• All differentiated cells contain the entire
  genome their specific characteristics arise from
  differential gene expression.

55
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Cellular therapy is a new approach to diseases
  that involve degeneration of one cell type.
• Alzheimers disease involves degeneration of
  neurons in the brain.
• If other cells could be made to differentiate
  into neurons, they could be transferred to the
  patient.

56
Figure 16.10 Expression of Specific
Transcription Factors Turns Fibroblasts into
Neurons
57
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• How do eukaryotes coordinate expression of sets
  of genes?
• Most have their own promoters, and may be far
  apart in the genome.
• If the genes have common regulatory sequences,
  they can be regulated by the same transcription
  factors.

58
16.2 How Is Eukaryotic Gene Transcription
Regulated?

• Plants in drought stress must synthesize several
  proteins (the stress response). The genes are
  scattered throughout the genome.
• Each of the genes has a regulatory sequence
  called stress response element (SRE). A
  transcription factor binds to this element and
  stimulates mRNA synthesis.

59
Figure 16.11 Coordinating Gene Expression
60
Working with Data 16.1 Expression of
Transcription Factors Turns Fibroblasts into
Neurons

• To determine whether specific transcription
  factors might change one type of cell to another,
  genes for transcription factors in neurons were
  inserted into fibroblasts.
• When five transcription factors were introduced
  into fibroblasts and expressed from very strong
  promoters, the fibroblasts became neurons.

61
Working with Data 16.1 Expression of
Transcription Factors Turns Fibroblasts into
Neurons

• Three main criteria were used to determine that
  the transformed cells were neurons
• Morphology
• Electrical excitability
• Lack of cell division

62
Working with Data 16.1 Expression of
Transcription Factors Turns Fibroblasts into
Neurons

• Question 1
• Neurons respond to electrical stimulation by
  generating an action potential. The electrical
  activity of a stimulated transformed fibroblast
  cell is shown in Fig. A 8, 12, and 20 days after
  addition of the transcription factors.
• What is the magnitude of the action potential of
  the transformed cell in millivolts?
• Look at Figure 45.10. How does this compare?

63
Working with Data 16.1, Figure A
64
Figure 45.10 The Course of an Action Potential
65
Working with Data 16.1 Expression of
Transcription Factors Turns Fibroblasts into
Neurons

• Question 2
• The rate of cell division in the population of
  transformed cells was measured by the
  incorporation of the labeled nucleotide BrdU into
  their DNA.
• The percentage of labeledand hence
  dividingcells is shown in Fig. B.
• Did cell division stop in the transformed cells?
  Explain your answer.

66
Working with Data 16.1, Figure B
67
16.3 How Do Viruses Regulate Their Gene
Expression?

• Viruses are infectious agents that infect
  cellular organisms, and cant reproduce outside
  their host cells.
• A bacterial virus (bacteriophage) injects its
  genetic material into a host cell and turns that
  cell into a virus factory.
• Other viruses enter cells and then shed their
  coats and take over the cells replication
  machinery.

68
16.3 How Do Viruses Regulate Their Gene
Expression?

• Virus particles, called virions, consist of DNA
  or RNA, a protein coat, and sometimes a lipid
  envelope.
• Viral genomes contain sequences that encode
  regulatory proteins that hijack the host cells
  transcriptional machinery.

69
16.3 How Do Viruses Regulate Their Gene
Expression?

• The viral lytic cyclehost cell lyses and
  releases progeny viruses.
• A phage injects a host cell with genetic material
  that takes over synthesis.
• New phage particles appear rapidly and are soon
  released from the lysed cell.

70
Figure 16.12 Bacteriophage and Host
71
16.3 How Do Viruses Regulate Their Gene
Expression?

• The lytic cycle has two stages.
• 1. Early stage viral promoter binds host RNA
  polymerase. Viral genes adjacent to this promoter
  are transcribed (positive regulation).

72
16.3 How Do Viruses Regulate Their Gene
Expression?

• Early genes encode proteins that shut down host
  transcription (negative regulation) and stimulate
  viral genome replication and transcription of
  viral late genes (positive regulation).
• Three minutes after DNA entry, viral nuclease
  enzymes digest the hosts chromosome, providing
  nucleotides for the synthesis of viral genomes.

73
Figure 16.13 The Lytic Cycle A Strategy for
Viral Reproduction
74
16.3 How Do Viruses Regulate Their Gene
Expression?

• 2. Late stage viral late genes are transcribed
  (positive regulation).
• They encode the viral capsid proteins and
  enzymes to lyse the host cell.
• The whole process from binding and infection to
  release of new particles takes about 30 minutes.

75
16.3 How Do Viruses Regulate Their Gene
Expression?

• Some viruses have evolved lysogenythe lytic
  cycle is delayed.
• Viral DNA integrates with the host DNA to form a
  prophage.
• As the host cell divides, the viral DNA
  replicates too and can last for thousands of
  generations.

76
Figure 16.14 The Lytic and Lysogenic Cycles of
Bacteriophages
77
16.3 How Do Viruses Regulate Their Gene
Expression?

• If a host cell is not growing well, the virus may
  switch to the lytic cycle.
• The prophage excises itself from the host
  chromosome and reproduces.
• Understanding the regulation of gene expression
  that underlies the lysis/lysogeny switch was a
  major achievement.

78
16.3 How Do Viruses Regulate Their Gene
Expression?

• How does the prophage know when to switch?
• Two virus genes encode regulatory proteins cI and
  Cro.
• cI blocks expression of genes for the lytic cycle
  and promotes expression of genes for lysogeny
  Cro has the opposite effect.

79
16.3 How Do Viruses Regulate Their Gene
Expression?

• If conditions are favorable for host cell growth,
  cI accumulates and outcompetes Cro for DNA
  binding phage enters lysogenic cycle.
• If host cell is under stress, cI is degraded and
  no longer blocks expression of Cro phage enters
  lytic cycle.

80
Figure 16.15 Control of Bacteriophage ? Lysis
and Lysogeny
81
16.3 How Do Viruses Regulate Their Gene
Expression?

• cI protein is degraded because it is structurally
  similar to E. coli protein LexA that is also
  degraded.
• LexA represses DNA repair mechanisms under normal
  conditions, but is degraded by other proteins
  when the cell is stressed.

82
16.3 How Do Viruses Regulate Their Gene
Expression?

• Eukaryote viruses
• DNA viruses Double- or single-stranded
  (complementary strand is made in the host cell)
• Some have both lytic and lysogenic life cycles.
• Examples Herpes viruses and papillomaviruses
  (warts).

83
16.3 How Do Viruses Regulate Their Gene
Expression?

• RNA viruses Usually single-stranded
• RNA is translated by the host cell to make viral
  proteins involved in RNA replication.
• Example Influenza virus.

84
16.3 How Do Viruses Regulate Their Gene
Expression?

• Retroviruses RNA virus with a gene for reverse
  transcriptasesynthesizes DNA from an RNA
  template.
• The DNA copy is inserted into the host genome.
• Example Human immunodeficiency virus (HIV).

85
16.3 How Do Viruses Regulate Their Gene
Expression?

• HIV regulation occurs at the elongation stage of
  transcription.
• HIV is an enveloped virusenclosed in a
  phospholipid membrane derived from the host.
• The envelope fuses with the host cell membrane,
  the virus enters, and its capsid is broken down.

86
Figure 16.16 The Reproductive Cycle of HIV
87
16.3 How Do Viruses Regulate Their Gene
Expression?

• Reverse transcriptase uses the viral RNA to make
  a complementary DNA (cDNA) strand.
• A copy of the cDNA is also made, and the
  double-stranded cDNA is inserted into host
  chromosome by integrase. The inserted DNA is
  called a provirus.

88
16.3 How Do Viruses Regulate Their Gene
Expression?

• The provirus resides permanently in the host
  chromosome, and can be inactive (latent) for
  years.
• Transcription of viral DNA is initiated, but host
  cell proteins prevent elongation.

89
Figure 16.17 Regulation of Transcription by HIV
(Part 1)
90
16.3 How Do Viruses Regulate Their Gene
Expression?

• Under certain conditions, transcription
  initiation increases, and some viral RNA is made,
  including RNA for a protein called tat
  (transactivator of transcription).
• tat binds to the viral RNA and production of
  full-length viral RNA is dramatically increased.
  The rest of the viral life cycle then proceeds.

91
Figure 16.17 Regulation of Transcription by HIV
(Part 2)
92
16.3 How Do Viruses Regulate Their Gene
Expression?

• Nearly every step in the HIV life cycle is a
  potential target for anti-HIV drugs
• Reverse transcriptase inhibitors (step 2)
• Integrase inhibitors (step 3)
• Protease inhibitors block posttranslational
  processing of viral proteins (step 5)

93
16.3 How Do Viruses Regulate Their Gene
Expression?

• Combinations of drugs have been very successful
  at treating HIV infection, but new strains
  rapidly emerge.
• New drugs are being developed to target other
  life cycle steps, including drugs that interfere
  with binding of virus to host cell, and interfere
  with tat activity.

94
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Epigenetics is the study of changes in gene
  expression that occur without changes in the DNA
  sequence.
• These changes are reversible, but sometimes
  stable and heritable.
• Includes two processes DNA methylation and
  chromosomal protein alterations.

95
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Methylation
• A methyl group is covalently added to the 5'
  carbon of cytosine, forming 5-methylcytosine
• Catalyzed by DNA methyltransferase
• Usually occurs in regions rich in C and G
  doublets, called CpG islandsoften in promoters

96
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• It can be heritable when DNA replicates, a
  maintenance methylase catalyzes formation of
  5-methylcytosine in the new strand.
• Or, the methylation pattern may be altered
  because it is reversible.
• Demethylase catalyzes removal of methyl groups.

97
Figure 16.18 DNA Methylation An Epigenetic
Change (Part 1)
98
Figure 16.18 DNA Methylation An Epigenetic
Change (Part 2)
99
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Effects of DNA methylation
• Methyl groups in promoter regions attract
  proteins for transcription repression. Methylated
  genes are often inactive
• In development, early demethylation allows many
  genes to become active
• Later, some genes may be silenced by
  methylation

100
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Silent genes may be turned back on
• DNA methylation can play a role in
  canceroncogenes get activated and promote cell
  division, and tumor suppressor genes can be
  turned off.

101
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Chromosomal protein alterations or chromatin
  remodeling
• DNA is packaged with histone proteins into
  nucleosomes. The DNA is inaccessible to RNA
  polymerase and transcription factors.
• The histones have tails with positively charged
  amino acids, which are attracted to negatively
  charged DNA.

102
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Histone acetyltransferases add acetyl groups to
  the tails which changes their charges, and opens
  up the nucleosome to activate transcription.

103
Figure 16.19 Epigenetic Remodeling of Chromatin
for Transcription
104
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Histone deacetylases removes the acetyl groups,
  which represses transcription.
• In some cancers, genes that inhibit cell division
  are excessively deacetylated.
• Drugs that inhibit histone deacetylase may be
  useful to treat the cancer.

105
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Histones can also be modified by
• Methylationinactivates genes
• Phosphorylationeffects depend on which amino
  acids are involved
• All the epigenetic effects are reversible, so
  gene activity may be determined by very complex
  patterns of histone modification.

106
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Environmental factors can induce epigenetic
  changes
• Monozygotic (identical) twins have identical
  genomes, and have been used to study epigenetic
  effects.
• In 3-year-old twins, DNA methylation patterns are
  the same. By age 50, when twins have been living
  apart in different environments, methylation
  patterns were quite different.

107
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Genomic imprinting
• In mammals, eggs and sperm develop different
  methylation patterns.
• For about 200 genes, offspring inherit an
  inactive (methylated) copy and an active
  (demethylated) one.

108
Figure 16.20 Genomic Imprinting
109
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Example of imprinting a region on human
  chromosome 15 called 15q11
• Rarely, a chromosome deletion results in the baby
  having only the male or female version of the
  gene.
• Male pattern results in Angelman syndrome, with
  epilepsy, tremors, and constant smiling

110
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Female pattern results in Prader-Willi syndrome,
  marked by muscle weakness and obesity
• The gene sequences are the same in both cases
  the epigenetic patterns are different.

111
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Patterns of DNA methylation may include large
  regions or whole chromosomes.
• Two kinds of chromatin
• Euchromatindiffuse, light-staining contains DNA
  that is transcribed
• Heterochromatincondensed, dark-staining,
  contains genes not transcribed

112
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• One type of heterochromatin is the inactive X
  chromosome in mammals.
• Males (XY) and females (XX) contain different
  numbers of X-linked genes, yet for most genes
  transcription rates are similar.
• Early in development, one of the X chromosomes in
  females is inactivated.

113
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• Which X chromosome gets inactivated is random in
  each cell.
• The inactivated X chromosome is heterochromatin,
  and shows up as a Barr body in human female
  cells.
• The DNA is heavily methylated, and unavailable
  for transcription, except for the Xist gene.

114
Figure 16.21 X Chromosome Inactivation
115
16.4 How Do Epigenetic Changes Regulate Gene
Expression?

• RNA transcribed from Xist (X inactivation-specific
  transcript) binds to the chromosome, spreading
  the inactivation.
• This RNA is an example of interference RNA.

116
Figure 16.21 X Chromosome Inactivation
117
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• After transcription, eukaryotic gene expression
  can be regulated in the nucleus before mRNA
  export, or after mRNA leaves.
• Control mechanisms include alternative splicing
  of pre-mRNA, gene silencing, translation
  repressors, and regulation of protein breakdown.

118
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Alternative splicing different mRNAs can be made
  from the same gene.
• Introns are spliced out mature mRNAs have none.
• Sometimes exons are spliced out tooresulting in
  different proteins.
• There are many more human mRNAs than there are
  coding genes.

119
Figure 16.22 Alternative Splicing Results in
Different Mature mRNAs and Proteins
120
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• MicroRNAs(miRNAs) small RNAs produced by
  noncoding regions of DNA.
• First found in C. elegans. Two genes effect
  transition through the larval stages
• Mutations in lin-14 caused the worm to skip the
  1st stage normal role is to facilitate stage 1
  events.

121
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• lin-4 mutations caused some cells to repeat a
  development pattern normally shown in the 1st
  stage its normal role is negative regulation of
  lin-14.
• lin-14 encodes a transcription factor that
  affects genes involved in larval cell
  progression.
• lin-4 encodes a 22-base miRNA that inhibits
  lin-14 expression post-transcriptionally, by
  binding to its mRNA.

122
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• The human genome has about 1,000 miRNA encoding
  regions.
• miRNAs can inhibit translation by binding to
  target mRNAs. Each one is about 22 bases long and
  has many targets, as binding doesnt have to be
  perfect.

123
Figure 16.23 mRNA Inhibition by RNAs (Part 1)
124
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Small interfering RNAs (siRNAs) also result in
  RNA silencing.
• Often arise from viral infection and transposon
  sequences. They bind to target mRNA and cause its
  degradation.
• May have evolved as defense to prevent
  translation of viral and transposon sequences.

125
Figure 16.23 mRNA Inhibition by RNAs (Part 2)
126
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Cells have two major ways to control the amount
  of protein after transcription
• Block mRNA translation
• Alter how long new proteins persist in the cell

127
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Translation can be altered by
• miRNAs that inhibit translation
• GTP cap on 5' end of mRNA can be modifiedif cap
  is unmodified mRNA is not translated
• Repressor proteins can block translation directly

128
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Translational repressor proteins can bind to
  noncoding regions of mRNA and block translation
  by preventing it from binding to a ribosome.
• The RNA region that is bound by the repressor is
  called a riboswitch.

129
Figure 16.24 Translational Repressor Can Repress
Translation
130
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Protein longevity
• Protein content of a cell is a function of
  synthesis and degradation.
• Proteins can be targeted for destruction when
  ubiquitin attaches to it and attracts other
  ubiquitins, forming a polyubiquitin chain.

131
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• The complex binds to a proteasomea large complex
  where the ubiquitin is removed and the protein is
  digested by proteases.

132
Figure 16.25 A Proteasome Breaks Down Proteins
133
16.5 How Is Eukaryotic Gene Expression Regulated
After Transcription?

• Some strains of human papillomavirus (HPV) add
  ubiquitin to p53 and retinoblastoma proteins,
  targeting them for degradation.
• These proteins normally inhibit the cell cycle,
  so the result of this HPV activity is unregulated
  cell division (cancer).

134
16 Answer to Opening Question

• Epigenetic changes often involve methylation.
• Some nutrients, such as folic acid, have methyl
  groups and participate in DNA modification.
• Experiments with mice show that diets rich in
  these nutrients change epigenetic patterns that
  remain throughout life.