Transcript Ch19

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
• Two features of eukaryotic genomes are a major
information-processing challenge:
– First, the typical eukaryotic genome is much
larger than that of a prokaryotic cell
– Second, cell specialization limits the
expression of many genes to specific cells
• The DNA-protein complex, called chromatin, is
ordered into higher structural levels than the DNAprotein complex in prokaryotes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
• The association of DNA and histones seems to
remain intact throughout the cell cycle
• In electron micrographs, unfolded chromatin has
the appearance of beads on a string
• Each “bead” is a nucleosome, the basic unit of
DNA packing
Animation: DNA Packing
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LE 19-2a
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
Linker DNA
(“string”)
Nucleosome
(“bead”)
Nucleosomes (10-nm fiber)
10 nm
Higher Levels of DNA Packing
• The next level of packing forms the 30-nm
chromatin fiber
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LE 19-2b
30 nm
Nucleosome
30-nm fiber
• In turn, the 30-nm fiber forms looped domains,
making up a 300-nm fiber
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LE 19-2c
Protein scaffold
Loops
300 nm
Looped domains (300-nm fiber)
Scaffold
• In a mitotic chromosome, the looped domains coil
and fold, forming the metaphase chromosome
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LE 19-2d
700 nm
1,400 nm
Metaphase chromosome
• Interphase chromatin is usually much less
condensed than that of mitotic chromosomes
• Much of the interphase chromatin is present as a
10-nm fiber, and some is 30-nm fiber, which in
some regions is folded into looped domains
• Interphase chromosomes have highly condensed
areas, called heterochromatin, and less
compacted areas, called euchromatin
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
• A multicellular organism’s cells undergo cell
differentiation, specialization in form and function
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Differential Gene Expression
• Differences between cell types result from
differential gene expression, the expression of
different genes by cells within the same genome
• In each type of differentiated cell, a unique subset
of genes is expressed
• Many key stages of gene expression can be
regulated in eukaryotic cells
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-3
Signal
NUCLEUS
Chromatin
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intro
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein
Regulation of Chromatin Structure
• Genes within highly packed heterochromatin are
usually not expressed
• Chemical modifications to histones and DNA of
chromatin influence both chromatin structure and
gene expression
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Histone Modification
• In histone acetylation, acetyl groups are attached
to positively charged lysines in histone tails
• This process seems to loosen chromatin structure,
thereby promoting the initiation of transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-4
Histone
tails
DNA
double helix
Amino acids
available
for chemical
modification
Histone tails protrude outward from a nucleosome
Unacetylated histones
Acetylated histones
Acetylation of histone tails promotes loose chromatin
structure that permits transcription
DNA Methylation
• DNA methylation, the addition of methyl groups to
certain bases in DNA, is associated with reduced
transcription in some species
• In some species, DNA methylation causes longterm inactivation of genes in cellular differentiation
• In genomic imprinting, methylation turns off either
the maternal or paternal alleles of certain genes at
the start of development
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Epigenetic Inheritance
• Although the chromatin modifications just
discussed do not alter DNA sequence, they may
be passed to future generations of cells
• The inheritance of traits transmitted by
mechanisms not directly involving the nucleotide
sequence is called epigenetic inheritance
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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 control
elements, segments of noncoding DNA that help
regulate transcription by binding certain proteins
• Control elements and the proteins they bind are
critical to the precise regulation of gene
expression in different cell types
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-5
Enhancer
(distal control elements)
Proximal
control elements
Exon
Intron
Exon
Poly-A signal Termination
sequence
region
Intron Exon
DNA
Upstream
Downstream
Promoter
Primary RNA
transcript
5
(pre-mRNA)
Transcription
Exon
Intron
Intron RNA
Poly-A signal
Exon
Intron Exon
Cleaved 3 end
of primary
transcript
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Coding segment
mRNA
3
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
• General transcription factors are essential for the
transcription of all protein-coding genes
• In eukaryotes, high levels of transcription of
particular genes depend on control elements
interacting with specific 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
• An activator is a protein that binds to an enhancer
and stimulates transcription of a gene
Animation: Initiation of Transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-6
Distal control
element
Activators
Promoter
Gene
DNA
TATA
box
Enhancer
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
Initiation complex
RNA synthesis
• Some transcription factors function as repressors,
inhibiting expression of a particular gene
• Some activators and repressors act indirectly by
influencing chromatin structure
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LE 19-7
Liver cell
nucleus
Available
activators
Enhancer
Control
elements
Lens cell
nucleus
Available
activators
Promoter
Albumin
gene
Crystallin
gene
Albumin
gene not
expressed
Albumin
gene
expressed
Crystallin gene
not expressed
Liver cell
Crystallin gene
expressed
Lens cell
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
• Transcription alone does not account for gene
expression
• More and more examples are being found of
regulatory mechanisms that operate at various
stages after transcription
• Such mechanisms allow a cell to fine-tune gene
expression rapidly in response to environmental
changes
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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
Animation: RNA Processing
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LE 19-8
Exons
DNA
Primary
RNA
transcript
RNA splicing
mRNA
or
mRNA Degradation
• The life span of mRNA molecules in the cytoplasm
is a key to determining the protein synthesis
• The mRNA life span 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
• The phenomenon of inhibition of gene expression
by RNA molecules is called RNA interference
(RNAi)
Animation: Blocking Translation
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Animation: mRNA Degradation
LE 19-9
Protein
complex
Degradation of mRNA
Dicer
OR
miRNA
Target mRNA
Hydrogen
bond
Blockage of translation
Initiation of Translation
• The initiation of translation of selected
mRNAs can be blocked by regulatory proteins that
bind to sequences or structures of the mRNA
• Alternatively, translation of all 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
• Proteasomes are giant protein complexes that
bind protein molecules and degrade them
Animation: Protein Processing
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Animation: Protein Degradation
LE 19-10
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Protein entering a
proteasome
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 are very same systems that play important
roles in embryonic development
• Thus, research into the molecular basis of cancer
has benefited from and informed many other fields
of biology
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Types of Genes Associated with Cancer
• Genes that normally regulate cell growth and
division during the cell cycle include:
– Genes for growth factors
– Their receptors
– Intracellular molecules of signaling pathways
• Mutations altering any of these genes in somatic
cells can lead to cancer
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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
• A DNA change that makes a proto-oncogene
excessively active converts it to an oncogene,
which may promote excessive cell division and
cancer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-11
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
Point mutation
within a control
element
Oncogene
Normal growth-stimulating
protein in excess
Normal growth-stimulating
protein in excess
Point mutation
within the gene
Oncogene
Hyperactive or
degradationresistant protein
Tumor-Suppressor Genes
• Tumor-suppressor genes encode proteins that
inhibit abnormal cell division
• Any decrease in the normal activity of a tumorsuppressor protein may contribute to cancer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Interference with Normal Cell-Signaling Pathways
• Many proto-oncogenes and tumor suppressor
genes encode components of growth-stimulating
and growth-inhibiting pathways, respectively
• We will focus on products of two genes, the ras
proto-oncogene and p53 tumor-suppressor gene
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The Ras protein, encoded by the ras gene, is a G
protein that relays a signal from a growth factor
receptor to a cascade of protein kinases
• Many ras oncogenes have a mutation that leads to
a hyperactive Ras protein that issues signals on its
own, resulting in excessive cell division
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-12_1
MUTATION
Growth
factor
Hyperactive
Ras protein
(product of
oncogene
issues signals
on its own.
G protein
Cell cycle-stimulating
pathway
Receptor
Protein kinases
(phosphorylation
cascade)
NUCLEUS
Transcription
factor (activator)
DNA
Gene expression
Protein that
stimulates
the cell cycle
• The p53 gene encodes a tumor-suppressor
protein that is a specific transcription factor that
promotes synthesis of cell cycle–inhibiting proteins
• Named for its 53,000-dalton protein product, the
p53 gene is often called the “guardian angel of the
genome”
• Mutations that knock out the p53 gene can lead to
excessive cell growth and cancer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-12_2
MUTATION
Growth
factor
Hyperactive
Ras protein
(product of
oncogene)
issues signals
on its own
G protein
Cell cycle-stimulating
pathway
Receptor
Protein kinases
(phosphorylation
cascade)
NUCLEUS
Transcription
factor (activator)
DNA
Gene expression
Protein that
stimulates
the cell cycle
Cell cycle-inhibiting
pathway
Protein kinases
MUTATION
UV
light
Active
form
of p53
DNA damage
in genome
DNA
Protein that
inhibits
the cell cycle
Defective or
missing
transcription
factor, such as
p53, cannot
activate
transcription
• Increased cell division, possibly leading to cancer,
can result if the cell cycle is overstimulated (as in
Figure 19.12a) or not inhibited when it normally
would be (as in Figure 19.12b)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-12_3
MUTATION
Growth
factor
Hyperactive
Ras protein
(product of
oncogene)
issues signals
on its own
G protein
Cell cycle-stimulating
pathway
Receptor
Protein kinases
(phosphorylation
cascade)
NUCLEUS
Transcription
factor (activator)
DNA
Gene expression
Protein that
stimulates
the cell cycle
Cell cycle-inhibiting
pathway
Protein kinases
MUTATION
Defective or
missing
transcription
factor, such as
p53, cannot
activate
transcription
Active
form
of p53
UV
light
DNA damage
in genome
DNA
Protein that
inhibits
the cell cycle
Effects of
mutations
EFFECTS OF MUTATIONS
Protein overexpressed
Cell cycle overstimulate
Protein absent
Increased cell
division
Cell cycle not
inhibited
The Multistep Model of Cancer Development
• More than one somatic mutation is generally
needed to produce a full-fledged cancer cell
• About a half dozen DNA changes must occur for a
cell to become fully cancerous
• These changes usually include at least one active
oncogene and mutation or loss of several tumorsuppressor genes
• Colorectal cancer, with 135,000 new cases and
60,000 deaths in the United States each year,
illustrates a multistep cancer path
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-13
Colon
Normal colon
epithelial cells
Loss of
tumorsuppressor
gene p53
Activation of
ras oncogene
Loss of
tumorsuppressor
Colon wall gene APC (or
other)
Small benign
growth (polyp)
Loss of
tumorsuppressor
gene DCC
Additional
mutations
Larger benign
growth (adenoma)
Malignant tumor
(carcinoma)
• Certain viruses promote cancer by integration of
viral DNA into a cell’s genome
• By this process, a retrovirus may donate an
oncogene to the cell
• Viruses seem to play a role in about 15% of
human cancer cases worldwide
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Inherited Predisposition to Cancer
• The fact that multiple genetic changes are
required to produce a cancer cell helps explain the
predispositions to cancer that run in some families
• Individuals who inherit a mutant oncogene or
tumor-suppressor allele have an increased risk of
developing certain types of cancer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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 much more noncoding DNA
– This is referred to as the “C-Paradox”
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• The sequencing of the human genome reveals
what makes up most of the 98.5% of the genome
that does not code for proteins, rRNAs, or tRNAs
• Most intergenic DNA is repetitive DNA, present in
multiple copies in the genome
• About three-fourths of repetitive DNA is made up
of transposable elements and sequences related
to them
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-14
Exons (regions of genes coding
for protein, rRNA, or tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Introns and
regulatory
sequences
(24%)
Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Unique
noncoding
DNA (15%)
Alu elements
(10%)
Simple sequence
DNA (3%)
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
• McClintock identified changes in the color of corn
kernels that made sense only by postulating that
some genetic elements move from other genome
locations into the genes for kernel color
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-16
Transposon
New copy of
transposon
DNA of genome
Transposon
is copied
Insertion
Mobile transposon
Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
DNA of genome
RNA
Insertion
Reverse
transcriptase
Retrotransposon movement
Sequences Related to Transposable Elements
• Multiple copies of transposable elements and
related sequences are scattered throughout the
eukaryotic genome
• In primates, a large portion of transposable
element–related DNA consists of a family of
similar sequences called Alu elements
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Other Repetitive DNA, Including Simple Sequence
DNA
• Simple sequence DNA contains many copies of
repeated short sequences
• Simple sequence DNA 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
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LE 19-17a
DNA
RNA transcripts
Non-transcribed
spacer
Transcription unit
DNA
18S
5.8S
28S
rRNA
5.8S
28S
18S
Part of the ribosomal RNA gene family
• The classic examples of multigene families of
nonidentical genes are two related families of
genes that encode globins
• Globin gene family clusters also include
pseudogenes, nonfunctional nucleotide
sequences that are similar to the functional genes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-17b
-Globin
Heme
Hemoglobin
a-Globin
a-Globin gene family
-Globin gene family
Chromosome 11
Chromosome 16

Embryo
 a a1 a2 a1
Fetus
and adult
 A
Embryo

Fetus
The human a-globin and -globin gene families


Adult
Concept 19.5: Duplications, rearrangements, and
mutations of DNA contribute to genome evolution
• The basis of change at the genomic level is
mutation, underlying much of genome evolution
• The earliest forms of life likely had a minimal
number of genes, including only those necessary
for survival and reproduction
• The size of genomes has increased over
evolutionary time, with the extra genetic material
providing raw material for gene diversification
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Duplication of Chromosome Sets
• Accidents in meiosis can lead to one or more extra
sets of chromosomes, a condition known as
polyploidy
• The genes in one or more of the extra sets can
diverge by accumulating mutations; these
variations may persist if the organism carrying
them survives and reproduces
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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 region
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-18
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologues
during meiosis
and
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
• After the duplication events, differences between
the genes in the globin family arose from
mutations that accumulated in the gene copies
over many generations
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-19
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies
a
Transposition
to different
chromosomes

a
Further
duplications
and mutations




a
 a a1 a2
a1 
a-Globin gene family
on chromosome 16


A


-Globin gene family
on chromosome 11

• Subsequent duplications of these genes and
random mutations gave rise to the present globin
genes, 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
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Evolution of Genes with Novel Functions
• The copies of some duplicated genes have
diverged so much in evolution that the functions of
their encoded proteins are now very different
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Rearrangements of Parts of Genes: Exon
Duplication and Exon Shuffling
• An exon can be duplicated on one chromosome
and deleted from the homologous chromosome
• In exon shuffling, errors in meiotic recombination
lead to some mixing and matching of exons, either
within a gene or between two nonallelic genes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-20
EGF
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons (green)
Exon
shuffling
F
F
F
Fibronectin gene with multiple
“finger” exons (orange)
F
F
EGF
Exon
duplication
K
K
Plasminogen gene with a
“kringle” exon (blue)
Portions of ancestral genes
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 may generate beneficial new sequence
combinations
• Some mechanisms can alter functions of genes or
their patterns of expression and regulation
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings