Transcript Chapter 20 Regulation of Gene Expression in Eukaryotes

Chapter 19
Regulation of Gene Expression in
Eukaryotes
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Chapter Outline
Ways of Regulating Eukaryotic Gene Expression: An
Overview
Induction of Transcriptional Activity by Environmental
and Biological Factors
Molecular Control of Transcription in Eukaryotes
Posttranscriptional Regulation of Gene Expression by
RNA Interference
Gene Expression and Chromatin Organization
Activation and Inactivation of Whole Chromosomes
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Ways of Regulating Eukaryotic
Gene Expression: An Overview
Eukaryotic gene expression can be
regulated at the transcriptional,
processing, or translational levels.
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Eukaryotic Gene Expression
-Capping 5’ polyAed at 3”
-RNA Splicing
-Compartmentalization
-Regulation ?
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Controlled Transcription of DNA
Eukaryote:
Both intracellular signaling and intercellular
communication are important for transcriptional
regulation in eukaryotes (cell surface to nucleus).
Positive and negative regulator proteins called
transcription factors bind to specific regions of DNA
and stimulate or inhibit transcription.
Prokaryote:
Protein/DNA interaction: negative (lac repressor) and
positive ( CAP/cAMP)
RNA polymerase © John Wiley & Sons, Inc.
Alternate Splicing of RNA
Splicing:-removing introns-spliceosomes
Alternate splicing of transcripts makes it
possible for a single gene to encode several
polypeptides.
is a prominent mechanism to generate protein
diversity.
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Alternate Splicing of the Rat
Troponin T Gene
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Cytoplasmic Control of
mRNA Stability
mRNA degradation
mRNA stability is influenced by several
factors
– The poly(A) tail
– The sequence of the 3’UTR
– Chemical factors (e.g., hormones)
– Small interfering RNAs (siRNAs) or
microRNAs (miRNAs)
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Induction of Transcriptional Activity by
Environmental and Biological Factors
Eukaryotic gene expression can be induced
by environmental factors such as heat and
by signaling molecules such as hormones
and growth factors.
Lactose- inducer
bacteria
Tryptophan- repressor
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The Heat-Shock Genes (Proteins)
When organisms are subjected to the stress of high
temperature, they synthesize a group of proteins (the
heat-shock proteins) that help to stabilize the internal
cellular environment.
The expression of the heat-shock proteins is regulated
at the transcriptional level; transcription of the heatshock genes is induced by heat.
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Induction of the Drosophila hsp70
Gene by Heat Shock
36.7 to 37ºC
41 to 42ºC
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Regulation of Gene Expression
by Steroid Hormones
Transcription factors
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Regulation of Gene Expression
by Peptide Hormones
Signal transduction
(several)
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Hormone Response Elements
Hormone response elements (HREs)
are analogous to the heat-shock
response elements.
HREs are DNA specific sequences
located near the genes they regulate
that bind specific proteins that act as
transcription factors.
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Activation of Transcription by
Hormones
A steroid hormone/cytosolic receptor complex
binds to the HRE sequence to stimulate
transcription.
For peptide hormones, the receptor stays at
the cell membrane; the signal is conveyed
through the cytoplasm by other proteins,
causing a transcription factor to bind to a
regulatory sequence near a gene.
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Molecular Control of
Transcription in Eukaryotes
The transcription of eukaryotic genes is
regulated by interactions between
proteins and DNA sequences within
or near the genes.
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DNA Sequences that Control
Transcription
Basal transcription factors are proteins that
bind to specific DNA sequences within the
promoter to facilitate RNA polymerase
alignment.
Special transcription factors are proteins
that bind to response elements or to
sequences called enhancers that are located
near a gene and facilitate the action of basal
transcription factors and RNA polymerase.
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Properties of Enhancers
Enhancers act over relatively large distances.
The influence of an enhancer of gene
expression is independent of orientation.
The effects of enhancers are independent of
position. They may be upstream,
downstream, or within an intron.
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Tissue-Specific Enhancers of
the Drosophila yellow Gene
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There Are Several Types of
Transcription Factors
Basal factors (TFs) and RNA polymerase bind
to promoter and TATAA box.
Activators are proteins that recognize specific
short DNA sequences inducing the efficiency of
the promoters.
Co-activators are proteins required for a more
efficient transcription. They do not bind DNA.
Regulators of chromatin structure
Figure 25.2
Regulation of Transcription by
Enhancers
Proteins that bind to enhancers influence the
activity of proteins that bind to promoters,
including the basal transcription factors
and RNA polymerase.
These proteins are brought into contact with
one another by the mediator complex.
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Proteins That Control
Transcription
Transcription factors usually have two
domains (fragment) that may be in separate
parts of the molecule or overlapping
– A DNA binding domain that binds the enhancer
– A transcriptional activation domain
A transcription factor bound to an enhancer
element may interact with other proteins
bound at enhancers or with proteins bound at
the promoter to facilitate RNA polymerase
alignment.
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Structural Motifs (smaller fragment) of
Transcription Factors
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Anatomy of a Typical Eukaryotic Gene, with Its
Core Promoter and Proximal Control Region
-----control elements
Enhancer
Silencer
monocistronic
Model for Enhancer Action
Suppressor or silencer
DHAC: De-acetylase complex
MTC: Methyl transferase complex
Co-repressor
HAT: histone acetyl transferase
Co-activator
Remodeling complex
Combinatorial Model for Gene Expression
Post-transcriptional Regulation of
Gene Expression by RNA
Interference
Short noncoding RNAs may regulate
the expression of eukaryotic genes by
interacting with the messenger RNAs
produced by these genes.
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RNA Interference
Small, noncoding RNAs base pair with target
sequences in mRNA.
The small RNAs interfere with expression of
the target mRNAs.
RNAi has been documented in C. elegans,
Drosophila, Arabidopsis, and in mammals,
including humans.
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MicroRNAs
 Some molecules that
induce RNAi are
derived from microRNA
(mir) genes.
 The mir transcript forms
a stem-loop structure
that is processed by the
enzymes Drosha and
Dicer to form an miRNA
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Sources of siRNA and miRNA
miRNAs are derived from endogenous
transcripts of the mir genes.
Long double-stranded RNA that is transfected
or injected into a cell can be processed to form
an siRNA. This can be used experimentally to
knock down expression of a gene.
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Gene Expression and
Chromatin Organization
Various aspects of chromatin
organization influence the
transcription of genes.
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Chromatin packaging: Eu- or hetero-chromatin
Position-effect variegation:
change in the position of the interaction of DNA/histones may
move the conversion of eu- to hetero-chromatin
Eye color phenotype
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Molecular Organization of
Transcriptionally Active DNA
Transcriptionally active DNA is more sensitive to
DNase I than non-transcribed DNA.
The nuclease sensitivity of transcriptionally active
genes depends on the presence of two small
nonhistone proteins, HMG14 and HMG17.
The promoter and enhancer regions of active genes
contain DNase I hypersensitive sites.
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The -Globin Gene Cluster
 The locus control region (LCR)
contains several DNase I
hypersensitive sites.
 The -globin genes are spatially
and temporally regulated.
 The LCR is dependent on
orientation, unlike enhancer
elements.
 The LCR insulates the -globin
genes from nearby chromatin.
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Chromatin Remodeling
In preparation for transcription,
nucleosomes are altered by
multiprotein complexes in a process
called chromatin remodeling.
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Types of Chromatin
Remodeling Complexes
Histone acetyl transferases (HATs)
transfer acetyl groups to lysine side chains
on histone proteins.
Other remodeling complexes disrupt
nucleosome structure near a gene’s
promoter by sliding or transferring histone
octamers to new locations (e.g., the yeast
SNI/SNF complex)
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Reverse Remodeling
Active chromatin can be made inactive by
biochemical modifications to histones.
– Histone deacetylases (HDACs) remove acetyl
groups from histone proteins.
– Histone methyl transferases (HMTs) add methyl
groups to histone proteins.
DNA methyl transferases (DNMTs) add
methyl groups to nucleotides to inactivate
transcription.
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Euchromatin and
Heterochromatin
Heterochromatin stains deeply.
Euchromatin stains more lightly.
Euchromatin contains the majority of
eukaryotic genes.
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Chromatin Is Divided into
Euchromatin and Heterochromatin
Heterochromatin is more
densely packed than
euchromatin
Heterochromatin :
-permanently condensed
-consists in DNA sequence repeats (not
transcribed)
-reduced density of genes (inactivated)
-replicates at late states of the S phase.
-interacts with Histones
Regions of heterochromatin remain densely packed throughout interphase.
Types of Heterochromatin
Centric heterochromatin is located
around the centromeres.
Intercalary heterochromatin is
dispersed throughout eukaryotic
chromosomes.
Telomeric heterochromatin is located
at the ends of the chromosomes.
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DNA Methylation
 Most methylated
cytosines are found in
the dinucleotide
sequence CG, denoted
mCpG.
 The restriction enzyme
HpaII recognizes and
cleaves the sequence
CCGG, but cannot
cleave the sequence
when the second
cytosine is methylated.
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CpG Islands
CpG dinucleotides occur less often that expected in
mammalian genomes, probably due to mutation into
TpG dinucleotides over the course of evolution.
The distribution of CpG dinucleotides is uneven.
Most CpG islands are located near transcription
start sites; cytosines in these regions are rarely
methylated.
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Gene Expression Is Associated
with DNA De-methylation
Gene expression is associated with de-methylation
Me
Me
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.
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