1. Eukaryotic Genomes: Organization, Regulation, and Evolution
Chapter 19
Eukaryotic Genomes: Organization, Regulation, and Evolution

2. 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

3. Both prokaryotes and eukaryotes
Must alter their patterns of gene expression in response to changes in environmental conditions

4. Eukaryotic chromosomes
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

5. 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

6. (a) Nucleosomes (10-nm fiber)
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
10 nm
DNA double helix
Histone
tails
His-
tones
Linker DNA
(“string”)
Nucleosome
(“bad”)
Histone H1
(a) Nucleosomes (10-nm fiber)
Figure 19.2 a

7. Higher Levels of DNA Packing
The next level of packing
Forms the 30-nm chromatin fiber
Nucleosome
30 nm
(b) 30-nm fiber
Figure 19.2 b

8. (c) Looped domains (300-nm fiber)
The 30-nm fiber, in turn
Forms looped domains, making up a 300-nm fiber
Protein scaffold
300 nm
(c) Looped domains (300-nm fiber)
Loops
Scaffold
Figure 19.2 c

9. (d) Metaphase chromosome
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

10. In interphase cells
Most chromatin is in the highly extended form called euchromatin

11. During development of a multicellular organism
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

12. 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

13. Many key stages of gene expression
Can be regulated in eukaryotic cells
Figure 19.3
Signal
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethlation
Gene
DNA
Gene available
for transcription
RNA
Exon
Transcription
Primary transcript
RNA processing
Transport to cytoplasm
Intron
Cap
mRNA in nucleus
Tail
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypetide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein

14. Regulation of Chromatin Structure
Genes within highly packed heterochromatin
Are usually not expressed

15. (a) Histone tails protrude outward from a nucleosome
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
DNA
double helix
Amino acids
available
for chemical
modification
Histone
tails
Figure 19.4a
(a) Histone tails protrude outward from a nucleosome

16. Histone acetylation
Seems to loosen chromatin structure and thereby enhance transcription
Figure 19.4 b
(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription
Unacetylated histones
Acetylated histones

17. Addition of methyl groups to certain bases in DNA
DNA Methylation
Addition of methyl groups to certain bases in DNA
Is associated with reduced transcription in some species

18. Epigenetic Inheritance
Is the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

19. 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

20. 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)
Proximal
control elements
DNA
Upstream
Promoter
Exon
Intron
Poly-A signal
sequence
Termination
region
Transcription
Downstream
Poly-A
signal
Primary RNA
transcript
(pre-mRNA) 5
Intron RNA
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Coding segment P G
mRNA
5 Cap
5 UTR
(untranslated
region)
Start
codon
Stop
3 UTR
tail
Chromatin changes
RNA processing
degradation
Translation
Protein processing
and degradation
Cleared 3 end
of primary
transport
Figure 19.5

21. The Roles of Transcription Factors
To initiate transcription
Eukaryotic RNA polymerase requires the assistance of proteins called transcription factors

22. 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

23. An activator
Is a protein that binds to an enhancer and stimulates transcription of a gene
Distal control
element
Activators
Enhancer
Promoter
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
Mediator proteins
RNA
Polymerase II
RNA synthesis
Transcription
Initiation complex
Chromatin changes
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
A DNA-bending protein
brings the bound activators
closer to the promoter.
Other transcription factors,
mediator proteins, and RNA
polymerase are nearby. 2
Activator proteins bind
to distal control elements
grouped as an enhancer in
the DNA. This enhancer has
three binding sites. 1
The activators bind to
certain general transcription
factors and mediator
proteins, helping them form
an active transcription
initiation complex on the promoter. 3
Figure 19.6

24. Some specific transcription factors function as repressors
To inhibit expression of a particular gene
Some activators and repressors
Act indirectly by influencing chromatin structure

25. 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

26. Mechanisms of Post-Transcriptional Regulation
An increasing number of examples
Are being found of regulatory mechanisms that operate at various stages after transcription

27. 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 or
Figure 19.8

28. The life span of mRNA molecules in the cytoplasm
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

29. Blockage of translation
RNA interference by single-stranded microRNAs (miRNAs)
Can lead to degradation of an mRNA or block its translation
The micro-
RNA (miRNA)
precursor folds
back on itself,
held together
by hydrogen
bonds. 1 2
An enzyme
called Dicer moves
along the double-
stranded RNA,
cutting it into
shorter segments.
One strand of
each short double-
stranded RNA is
degraded; the other
strand (miRNA) then
associates with a
complex of proteins. 3
The bound
miRNA can base-pair
with any target
mRNA that contains
the complementary
sequence. 4
The miRNA-protein
complex prevents gene
expression either by
degrading the target
mRNA or by blocking
its translation. 5 5
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Degradation of mRNA OR
Blockage of translation
Target mRNA
miRNA
Protein
complex
Dicer
Hydrogen
bond
Figure 19.9

30. 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

31. Protein Processing and Degradation
After translation
Various types of protein processing, including cleavage and the addition of chemical groups, are subject to control

32. Proteasomes
Are giant protein complexes that bind protein molecules and degrade them
Enzymatic components of the
proteasome cut the protein into
small peptides, which can be
further degraded by other
enzymes in the cytosol. 3
The ubiquitin-tagged protein
is recognized by a proteasome,
which unfolds the protein and
sequesters it within a central cavity. 2
Multiple ubiquitin mol-
ecules are attached to a protein
by enzymes in the cytosol. 1
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Ubiquitin
Protein to
be degraded
Ubiquinated
protein
Proteasome
and ubiquitin
to be recycled
Protein
fragments
(peptides)
Protein entering a
proteasome
Figure 19.10

33. The gene regulation systems that go wrong during cancer
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

34. 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

35. Oncogenes and Proto-Oncogenes
Are cancer-causing genes
Proto-oncogenes
Are normal cellular genes that code for proteins that stimulate normal cell growth and division

36. 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
Point mutation
within a control
element
within the gene
Oncogene
Normal growth-stimulating
protein in excess
Hyperactive or
degradation-
resistant protein
New
promoter
Figure 19.11

37. Tumor-Suppressor Genes
Encode proteins that inhibit abnormal cell division

38. Interference with Normal Cell-Signaling Pathways
Many proto-oncogenes and tumor suppressor genes
Encode components of growth-stimulating and growth-inhibiting pathways, respectively

39. 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
Figure 19.12a
(a) Cell cycle–stimulating pathway.
This pathway is triggered by a growth
factor that binds to its receptor in the
plasma membrane. The signal is relayed to
a G protein called Ras. Like all G proteins, Ras
is active when GTP is bound to it. Ras passes
the signal to a series of protein kinases.
The last kinase activates 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. 1 2 4 3 5
GTP
Ras
Hyperactive
Ras protein
(product of
oncogene)
issues signals
on its own
NUCLEUS
Gene expression
Protein that
stimulates
the cell cycle P
MUTATION
DNA
G protein 3
Protein kinases
(phosphorylation
cascade) 4 2
Receptor
Transcription
factor (activator) 5

40. (b) Cell cycle–inhibiting pathway. In this
The p53 gene encodes a tumor-suppressor protein
That is a specific transcription factor that promotes the synthesis of cell cycle–inhibiting proteins UV
light
DNA
Defective or
missing
transcription
factor, such as
p53, cannot
activate
MUTATION
Protein that
inhibits
the cell cycle
pathway, DNA damage is an intracellular
signal that is passed via protein kinases
and leads to activation of 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.
(b) Cell cycle–inhibiting pathway. In this 1 3 2
Protein kinases 2 3
Active
form
of p53
DNA damage
in genome 1
Figure 19.12b

41. 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
Protein absent
Cell cycle
overstimulated
Increased cell
division
Cell cycle not
inhibited
Figure 19.12c

42. The Multistep Model of Cancer Development
Normal cells are converted to cancer cells
By the accumulation of multiple mutations affecting proto-oncogenes and tumor-suppressor genes

43. A multistep model for the development of colorectal cancer
Colon
Colon wall
Normal colon
epithelial cells
Small benign
growth (polyp)
Larger benign
growth (adenoma)
Malignant tumor
(carcinoma)
1 Loss of tumor-
suppressor
gene APC (or
other)
4 Loss of
tumor-suppressor
gene p53
2 Activation of
ras oncogene
3 Loss of
tumor-
suppressor
gene DCC
5 Additional
mutations
Figure 19.13

44. Certain viruses
Promote cancer by integration of viral DNA into a cell’s genome

45. Inherited Predisposition to Cancer
Individuals who inherit a mutant oncogene or tumor-suppressor allele
Have an increased risk of developing certain types of cancer

46. The bulk of most eukaryotic genomes
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

47. 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

48. 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%)
Introns and
regulatory
(24%)
Unique
noncoding
DNA (15%)
DNA
unrelated to
(about 15%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Large-segment
duplications (5-6%)
Figure 19.14

49. 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

50. 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
New copy of
transposon
is copied
DNA of genome
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
retrotransposon
RNA
Reverse
transcriptase
(b) Retrotransposon movement
Figure 19.16a, b

51. 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

52. Other Repetitive DNA, Including 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

53. 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

54. Some multigene families
Consist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA products
DNA
RNA transcripts
Non-transcribed
spacer
Transcription unit
18S
5.8S
28S
rRNA
Figure 19.17a Part of the ribosomal RNA gene family

55. 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
Embryo
Fetus
and adult
Adult  G A    
  2  1 
Figure 19.17b The human -globin and -globin gene families

56. The basis of change at the genomic level is mutation
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

57. 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

58. 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
Nonsister
chromatids
Transposable
element
Gene
Incorrect pairing
of two homologues
during meiosis
Crossover
and
Figure 19.18

59. 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      2 1   G A  
-Globin gene family
on chromosome 16
 -Globin gene family
on chromosome 11 
Evolutionary time
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes
Further duplications
and mutations
Figure 19.19

60. Subsequent duplications of these genes and random mutations
Gave rise to the present globin genes, all of which code for oxygen-binding proteins

61. The similarity in the amino acid sequences of the various globin proteins
Supports this model of gene duplication and mutation
Table 19.1

62. 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

63. 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

64. 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
Epidermal growth
factor gene with multiple
EGF exons (green) F
Fibronectin gene with multiple
“finger” exons (orange)
Exon
shuffling
duplication K
Plasminogen gene with a
“kfingle” exon (blue)
Portions of ancestral genes
TPA gene as it exists today
Figure 19.20

65. 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