Transcript Eukaryotic Genomes

Chapter 19
Eukaryotic Genomes:
Organization, Regulation, and
Evolution
PowerPoint Lectures for
Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Overview: How Eukaryotic Genomes Work and
Evolve
• In eukaryotes, the DNA-protein complex, called
chromatin
– Is ordered into higher structural levels than the
DNA-protein complex in prokaryotes
Figure 19.1
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• Both prokaryotes and eukaryotes
– Must alter their patterns of gene expression in
response to changes in environmental
conditions
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• Concept 19.1: Chromatin structure is based on
successive levels of DNA packing
• Eukaryotic DNA
– Is precisely combined with a large amount of
protein
• Eukaryotic chromosomes
– Contain an enormous amount of DNA relative
to their condensed length
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Nucleosomes, or “Beads on a String”
• Proteins called histones
– Are responsible for the first level of DNA
packing in chromatin
– Bind tightly to DNA
• The association of DNA and histones
– Seems to remain intact throughout the cell
cycle
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• In electron micrographs
– Unfolded chromatin has the appearance of beads
on a string
• Each “bead” is a nucleosome
– The basic unit of DNA packing
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
Linker DNA
(“string”)
Nucleosome
(“bad”)
(a) Nucleosomes (10-nm fiber)
Figure 19.2 a
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10 nm
Higher Levels of DNA Packing
• The next level of packing
– Forms the 30-nm chromatin fiber
30 nm
Nucleosome
(b) 30-nm fiber
Figure 19.2 b
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• The 30-nm fiber, in turn
– Forms looped domains, making up a 300-nm
fiber
Protein scaffold
Loops
300 nm
(c) Looped domains (300-nm fiber)
Figure 19.2 c
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Scaffold
• In a mitotic chromosome
– The looped domains themselves coil and fold
forming the characteristic metaphase
chromosome
700 nm
1,400 nm
(d) Metaphase chromosome
Figure 19.2 d
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• In interphase cells
– Most chromatin is in the highly extended form
called euchromatin
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• Concept 19.2: Gene expression can be
regulated at any stage, but the key step is
transcription
• All organisms
– Must regulate which genes are expressed at
any given time
• During development of a multicellular organism
– Its cells undergo a process of specialization in
form and function called cell differentiation
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Differential Gene Expression
• Each cell of a multicellular eukaryote
– Expresses only a fraction of its genes
• In each type of differentiated cell
– A unique subset of genes is expressed
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• Many key stages of gene expression
– Can be regulated in eukaryotic cells
Signal
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethlation
DNA
Gene available
for transcription
Gene
Transcription
RNA
Cap
Exon
Primary transcript
Intron
RNA processing
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypetide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Figure 19.3
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Degraded protein
Regulation of Chromatin Structure
• Genes within highly packed heterochromatin
– Are usually not expressed
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Histone Modification
• Chemical modification of histone tails
– Can affect the configuration of chromatin and
thus gene expression
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Histone
tails
DNA
double helix
Amino acids
available
for chemical
modification
Figure 19.4a
(a) Histone tails protrude outward from a nucleosome
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• Histone acetylation
– Seems to loosen chromatin structure and
thereby enhance transcription
Unacetylated histones
Figure 19.4 b
Acetylated histones
(b) Acetylation of histone tails promotes loose chromatin structure that
permits transcription
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DNA Methylation
• Addition of methyl groups to certain bases
in DNA
– Is associated with reduced transcription in
some species
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Epigenetic Inheritance
• Epigenetic inheritance
– Is the inheritance of traits transmitted by
mechanisms not directly involving the
nucleotide sequence
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Regulation of Transcription Initiation
• Chromatin-modifying enzymes provide initial
control of gene expression
– By making a region of DNA either more or less
able to bind the transcription machinery
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Organization of a Typical Eukaryotic Gene
• Associated with most eukaryotic genes are
multiple control elements
– Segments of noncoding DNA that help regulate
transcription by binding certain proteins
Enhancer
(distal control elements)
Poly-A signal Termination
sequence
region
Proximal
control elements
Exon
Intron
Exon
Intron
Exon
DNA
Downstream
Upstream
Promoter
Chromatin changes
Transcription
Exon
Primary RNA
5
transcript
(pre-mRNA)
Intron
Exon
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Transcription
Intron RNA
RNA processing
mRNA
degradation
Cleared 3 end
of primary
transport
Coding segment
Translation
Protein processing
and degradation
Poly-A
signal
Intron Exon
mRNA
G
P
Figure 19.5
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P
P
5 Cap 5 UTR
(untranslated
region)
Start
codon
Stop
codon
Poly-A
3 UTR
(untranslated tail
region)
The Roles of Transcription Factors
• To initiate transcription
– Eukaryotic RNA polymerase requires the
assistance of proteins called transcription
factors
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Enhancers and Specific Transcription Factors
• Proximal control elements
– Are located close to the promoter
• Distal control elements, groups of which are
called enhancers
– May be far away from a gene or even in
an intron
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• An activator
– Is a protein that binds to an enhancer and
stimulates transcription of a gene
Distal control
element
Activators
Enhancer
1 Activator proteins bind
to distal control elements
grouped as an enhancer in
the DNA. This enhancer has
three binding sites.
2 A DNA-bending protein
brings the bound activators
closer to the promoter.
Other transcription factors,
mediator proteins, and RNA
polymerase are nearby.
Promoter
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
Mediator proteins
RNA
Polymerase II
Chromatin changes
3 The activators bind to
certain general transcription
factors and mediator
proteins, helping them form
an active transcription
initiation complex on the promoter.
Transcription
RNA processing
mRNA
degradation
Figure 19.6
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RNA
Polymerase II
Translation
Protein processing
and degradation
Transcription
Initiation complex
RNA synthesis
• Some specific transcription factors function as
repressors
– To inhibit expression of a particular gene
• Some activators and repressors
– Act indirectly by influencing chromatin
structure
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Coordinately Controlled Genes
• Unlike the genes of a prokaryotic operon
– Coordinately controlled eukaryotic genes each
have a promoter and control elements
• The same regulatory sequences
– Are common to all the genes of a group,
enabling recognition by the same specific
transcription factors
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Mechanisms of Post-Transcriptional Regulation
• An increasing number of examples
– Are being found of regulatory mechanisms that
operate at various stages after transcription
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RNA Processing
• In alternative RNA splicing
– Different mRNA molecules are produced from the
same primary transcript, depending on which RNA
segments are treated as exons and which as
introns
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Exons
DNA
Primary
RNA
transcript
RNA splicing
Figure 19.8
mRNA
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or
mRNA Degradation
• The life span of mRNA molecules in the
cytoplasm
– Is an important factor in determining the
protein synthesis in a cell
– Is determined in part by sequences in the
leader and trailer regions
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• RNA interference by single-stranded microRNAs
(miRNAs)
– Can lead to degradation of an mRNA or block its
translation
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.
55 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
Figure 19.9
Hydrogen
bond
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Blockage of translation
Initiation of Translation
• The initiation of translation of selected
mRNAs
– Can be blocked by regulatory proteins that
bind to specific sequences or structures of the
mRNA
• Alternatively, translation of all the mRNAs
in a cell
– May be regulated simultaneously
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Protein Processing and Degradation
• After translation
– Various types of protein processing, including
cleavage and the addition of chemical groups,
are subject to control
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• Proteasomes
– Are giant protein complexes that bind protein
molecules and degrade them
3 Enzymatic components of the
1 Multiple ubiquitin molChromatin changes
ecules are attached to a protein
by enzymes in the cytosol.
2 The ubiquitin-tagged protein
is recognized by a proteasome,
which unfolds the protein and
sequesters it within a central cavity.
proteasome cut the protein into
small peptides, which can be
further degraded by other
enzymes in the cytosol.
Transcription
RNA processing
mRNA
degradation
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Translation
Proteasome
Protein processing
and degradation
Protein to
be degraded
Ubiquinated
protein
Protein entering a
proteasome
Figure 19.10
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Protein
fragments
(peptides)
• Concept 19.3: Cancer results from genetic
changes that affect cell cycle control
• The gene regulation systems that go wrong
during cancer
– Turn out to be the very same systems that play
important roles in embryonic development
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Types of Genes Associated with Cancer
• The genes that normally regulate cell growth
and division during the cell cycle
– Include genes for growth factors, their
receptors, and the intracellular molecules of
signaling pathways
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Oncogenes and Proto-Oncogenes
• Oncogenes
– Are cancer-causing genes
• Proto-oncogenes
– Are normal cellular genes that code for
proteins that stimulate normal cell growth and
division
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• A DNA change that makes a proto-oncogene
excessively active
– Converts it to an oncogene, which may promote
excessive cell division and cancer
Proto-oncogene
DNA
Translocation or transposition:
gene moved to new locus,
under new controls
Gene amplification:
multiple copies of the gene
New
promoter
Normal growth-stimulating
protein in excess
Normal growth-stimulating
protein in excess
Figure 19.11
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Point mutation
within a control
element
Point mutation
within the gene
Oncogene
Oncogene
Normal growth-stimulating
protein in excess
Hyperactive or
degradationresistant protein
Tumor-Suppressor Genes
• Tumor-suppressor genes
– Encode proteins that inhibit abnormal cell
division
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Interference with Normal Cell-Signaling Pathways
• Many proto-oncogenes and tumor suppressor
genes
– Encode components of growth-stimulating and
growth-inhibiting pathways, respectively
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• The Ras protein, encoded by the ras gene
– Is a G protein that relays a signal from a
growth factor receptor on the plasma
membrane to a cascade of protein kinases
1
Growth
factor
MUTATION
Ras
GTP
3
(a) Cell cycle–stimulating pathway.
This pathway is triggered by 1 a growth
factor that binds to 2 its receptor in the
plasma membrane. The signal is relayed to 3
a G protein called Ras. Like all G proteins, Ras
is active when GTP is bound to it. Ras passes
the signal to 4 a series of protein kinases.
The last kinase activates 5 a transcription
activator that turns on one or more genes
for proteins that stimulate the cell cycle. If a
mutation makes Ras or any other pathway
component abnormally active, excessive cell
division and cancer may result.
P
Ras
P
P
P
P
P
GTP
4
2
Receptor
G protein
Hyperactive
Ras protein
(product of
oncogene)
issues signals
on its own
Protein kinases
(phosphorylation
cascade)
NUCLEUS
5
Transcription
factor (activator)
DNA
Gene expression
Protein that
stimulates
the cell cycle
Figure 19.12a
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• The p53 gene encodes a tumor-suppressor
protein
– That is a specific transcription factor that
promotes the synthesis of cell cycle–inhibiting
proteins
(b) Cell cycle–inhibiting pathway. In this
pathway, 1 DNA damage is an intracellular
signal that is passed via 2 protein kinases
and leads to activation of 3 p53. Activated
p53 promotes transcription of the gene for a
protein that inhibits the cell cycle. The
resulting suppression of cell division ensures
that the damaged DNA is not replicated.
Mutations causing deficiencies in any
pathway component can contribute to the
development of cancer.
2
UV
light
Protein kinases
3
1
DNA damage
in genome
Active
form
of p53
DNA
Protein that
inhibits
the cell cycle
Figure 19.12b
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MUTATION
Defective or
missing
transcription
factor, such as
p53, cannot
activate
transcription
• Mutations that knock out the p53 gene
– Can lead to excessive cell growth and cancer
(c) Effects of mutations. Increased cell
division, possibly leading to cancer,
can result if the cell cycle is
overstimulated, as in (a), or not
inhibited when it normally would be,
as in (b).
EFFECTS OF MUTATIONS
Protein
overexpressed
Cell cycle
overstimulated
Figure 19.12c
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Protein absent
Increased cell
division
Cell cycle not
inhibited
The Multistep Model of Cancer Development
• Normal cells are converted to cancer cells
– By the accumulation of multiple mutations
affecting proto-oncogenes and tumorsuppressor genes
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• A multistep model for the development of
colorectal cancer
Colon
Colon wall
Normal colon
epithelial cells
1 Loss of tumorsuppressor
gene APC (or
other)
4 Loss of
tumor-suppressor
gene p53
2 Activation of
ras oncogene
Small benign
growth (polyp)
3 Loss of
tumorsuppressor
gene DCC
Figure 19.13
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Larger benign
growth (adenoma)
5 Additional
mutations
Malignant tumor
(carcinoma)
• Certain viruses
– Promote cancer by integration of viral DNA into
a cell’s genome
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Inherited Predisposition to Cancer
• Individuals who inherit a mutant oncogene or
tumor-suppressor allele
– Have an increased risk of developing certain
types of cancer
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• Concept 19.4: Eukaryotic genomes can have
many noncoding DNA sequences in addition to
genes
• The bulk of most eukaryotic genomes
– Consists of noncoding DNA sequences, often
described in the past as “junk DNA”
• However, much evidence is accumulating
– That noncoding DNA plays important roles in
the cell
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The Relationship Between Genomic Composition
and Organismal Complexity
• Compared with prokaryotic genomes, the
genomes of eukaryotes
– Generally are larger
– Have longer genes
– Contain a much greater amount of noncoding
DNA both associated with genes and between
genes
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• Now that the complete sequence of the human
genome is available
– We know what makes up most of the 98.5% that
does not code for proteins, rRNAs, or tRNAs
Exons (regions of genes coding
for protein, rRNA, tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Alu elements
(10%)
Figure 19.14
Simple sequence
DNA (3%)
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Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Large-segment
duplications (5-6%)
Transposable Elements and Related Sequences
• The first evidence for wandering DNA
segments
– Came from geneticist Barbara McClintock’s
breeding experiments with Indian corn
Figure 19.15
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Movement of Transposons and Retrotransposons
• Eukaryotic transposable elements are of two types
– Transposons, which move within a genome by
means of a DNA intermediate
– Retrotransposons, which move by means of an
RNA intermediate
Transposon
DNA of genome
Transposon
is copied
New copy of
transposon
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
DNA of genome
RNA
Reverse
transcriptase
Figure 19.16a, b
(b) Retrotransposon movement
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Insertion
Sequences Related to Transposable Elements
• Multiple copies of transposable elements and
sequences related to them
– Are scattered throughout the eukaryotic
genome
• In humans and other primates
– A large portion of transposable element–
related DNA consists of a family of similar
sequences called Alu elements
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Other Repetitive DNA, Including Simple Sequence DNA
• Simple sequence DNA
– Contains many copies of tandemly repeated
short sequences
– Is common in centromeres and telomeres,
where it probably plays structural roles in the
chromosome
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Genes and Multigene Families
• Most eukaryotic genes
– Are present in one copy per haploid set of
chromosomes
• The rest of the genome
– Occurs in multigene families, collections of
identical or very similar genes
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• Some multigene families
– Consist of identical DNA sequences, usually
clustered tandemly, such as those that code
for RNA products
RNA transcripts
DNA
Non-transcribed
spacer
Transcription unit
DNA
18S
5.8S
28S
rRNA
Figure 19.17a Part
of the ribosomal
RNA gene family
28S
18S
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5.8S
• The classic examples of multigene families of
nonidentical genes
– Are two related families of genes that encode
globins
-Globin
Heme
Hemoglobin
-Globin
-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11

Figure 19.17b The human
-globin and -globin
gene families
Embryo
  1 2 1
2
Fetus
and adult
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

G A
Embryo
Fetus



Adult
• Concept 19.5: Duplications, rearrangements,
and mutations of DNA contribute to genome
evolution
• The basis of change at the genomic level is
mutation
– Which underlies much of genome evolution
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Duplication of Chromosome Sets
• Accidents in cell division
– Can lead to extra copies of all or part of a
genome, which may then diverge if one set
accumulates sequence changes
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Duplication and Divergence of DNA Segments
• Unequal crossing over during prophase I of
meiosis
– Can result in one chromosome with a deletion and
another with a duplication of a particular gene
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologues
during meiosis
and
Figure 19.18
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Evolution of Genes with Related Functions: The
Human Globin Genes
• The genes encoding the various globin proteins
– Evolved from one common ancestral globin gene,
which duplicated and diverged
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes



Further duplications
and mutations


Figure 19.19


  2  2 1 
1
-Globin gene family
on chromosome 16
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


G

A

 -Globin gene family
on chromosome 11


• Subsequent duplications of these genes and
random mutations
– Gave rise to the present globin genes, all of
which code for oxygen-binding proteins
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• The similarity in the amino acid sequences of the
various globin proteins
– Supports this model of gene duplication and
mutation
Table 19.1
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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
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Rearrangements of Parts of Genes: Exon
Duplication and Exon Shuffling
• A particular exon within a gene
– Could be duplicated on one chromosome and
deleted from the homologous chromosome
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• In exon shuffling
– Errors in meiotic recombination lead to the
occasional mixing and matching of different exons
either within a gene or between two nonallelic
genes
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons (green)
EGF
Exon
shuffling
F
F
F
Exon
duplication
F
Fibronectin gene with multiple
“finger” exons (orange)
F
EGF
K
K
Plasminogen gene with a
“kfingle” exon (blue)
Figure 19.20
Portions of ancestral genes
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Exon
shuffling
TPA gene as it exists today
K
How Transposable Elements Contribute to Genome Evolution
• Movement of transposable elements or
recombination between copies of the same
element
– Occasionally generates new sequence
combinations that are beneficial to the
organism
• Some mechanisms
– Can alter the functions of genes or their
patterns of expression and regulation
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