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

2. 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 DNA-protein complex in prokaryotes

3. 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

4. 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

5. LE 19-2a 2 nm DNA double helix His- Histone tones tails 10 nm
Histone H1
10 nm
Linker DNA
(“string”)
Nucleosome
(“bead”)
Nucleosomes (10-nm fiber)

6. Higher Levels of DNA Packing
The next level of packing forms the 30-nm chromatin fiber

7. LE 19-2b
30 nm
Nucleosome
30-nm fiber

8. In turn, the 30-nm fiber forms looped domains, making up a 300-nm fiber

9. LE 19-2c Protein scaffold Loops 300 nm Scaffold
Looped domains (300-nm fiber)

10. In a mitotic chromosome, the looped domains coil and fold, forming the metaphase chromosome

11. LE 19-2d
700 nm
1,400 nm
Metaphase chromosome

12. 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

13. 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

14. 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

15. Chemical modification Degradation of protein
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

16. 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

17. 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

18. 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

19. 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 long- term 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

20. 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

21. 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

22. 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

23. (distal control elements)
Enhancer
(distal control elements)
Proximal
control elements
Poly-A signal
sequence
Termination
region
Exon
Intron
Exon
Intron
Exon
DNA
Upstream
Downstream
Promoter
Transcription
Poly-A signal
Primary RNA
transcript
(pre-mRNA)
Exon
Intron
Exon
Intron
Exon
Cleaved 3¢ end
of primary
transcript 5¢
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Intron RNA
Coding segment
mRNA 3¢
Start
codon
Stop
codon
5¢ Cap
5¢ UTR
(untranslated
region)
3¢ UTR
(untranslated
region)
Poly-A
tail

24. 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

25. 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

26. LE 19-6 Distal control element Activators Promoter Gene DNA Enhancer
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
Initiation complex
RNA synthesis

27. Some transcription factors function as repressors, inhibiting expression of a particular gene
Some activators and repressors act indirectly by influencing chromatin structure

28. LE 19-7 Liver cell nucleus Lens cell nucleus Available activators
Enhancer
Promoter
Control
elements
Albumin
gene
Albumin
gene not
expressed
Crystallin
gene
Albumin
gene
expressed
Crystallin gene
not expressed
Crystallin gene
expressed
Liver cell
Lens cell

29. 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

30. 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

31. Animation: 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

32. LE 19-8
Exons
DNA
Primary
RNA
transcript
RNA splicing or
mRNA

33. 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

34. Animation: Blocking Translation Animation: mRNA Degradation
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
Animation: mRNA Degradation

35. LE 19-9 Protein complex Degradation of mRNA Dicer OR miRNA Target mRNA
Hydrogen
bond
Blockage of translation

36. 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

37. 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
Animation: Protein Degradation

38. LE 19-10 Proteasome and ubiquitin to be recycled Ubiquitin Proteasome
Protein to
be degraded
Ubiquitinated
protein
Protein
fragments
(peptides)
Protein entering a
proteasome

39. 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

40. 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

41. 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

42. LE 19-11 Proto-oncogene DNA Point mutation within a control element
Translocation or transposition:
gene moved to new locus,
under new controls
Point mutation
within the gene
Gene amplification:
multiple copies of the gene
New
promoter
Oncogene
Oncogene
Normal growth-stimulating
protein in excess
Normal growth-stimulating
protein in excess
Normal growth-stimulating
protein in excess
Hyperactive or
degradation-
resistant protein

43. Tumor-Suppressor Genes
Tumor-suppressor genes encode proteins that inhibit abnormal cell division
Any decrease in the normal activity of a tumor- suppressor protein may contribute to cancer

44. 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

45. 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

46. LE 19-12_1 Growth factor G protein Cell cycle-stimulating pathway
MUTATION
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

47. 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

48. LE 19-12_2 MUTATION Cell cycle-stimulating pathway NUCLEUS
Growth
factor
MUTATION
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
Active
form
of p53 UV
light
DNA damage
in genome
DNA
Protein that
inhibits
the cell cycle

49. 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)

50. LE 19-12_3 Growth MUTATION factor G protein Cell cycle-stimulating
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
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
Protein absent
Cell cycle overstimulate
Increased cell
division
Cell cycle not
inhibited

51. 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 tumor- suppressor genes
Colorectal cancer, with 135,000 new cases and 60,000 deaths in the United States each year, illustrates a multistep cancer path

52. LE 19-13 Colon Loss of tumor- suppressor gene APC (or other)
Activation of
ras oncogene
Loss of
tumor-
suppressor
gene p53
Colon wall
Loss of
tumor-
suppressor
gene DCC
Additional
mutations
Normal colon
epithelial cells
Small benign
growth (polyp)
Larger benign
growth (adenoma)
Malignant tumor
(carcinoma)

53. 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

54. 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

55. 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

56. 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

57. 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

58. Exons (regions of genes coding for protein, rRNA, or tRNA) (1.5%)
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%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(about 15%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Large-segment
duplications (5–6%)

59. 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

60. 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

61. LE 19-16
New copy of
transposon
Transposon
DNA of genome
Transposon
is copied
Insertion
Mobile transposon
Transposon movement (“copy-and-paste” mechanism)
New copy of
retrotransposon
Retrotransposon
DNA of genome
RNA
Insertion
Reverse
transcriptase
Retrotransposon movement

62. 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

63. 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

64. 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

65. Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA products

66. Part of the ribosomal RNA gene family
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

67. 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

68. The human a-globin and b-globin gene families
LE 19-17b
Heme
-Globin
Hemoglobin
a-Globin
a-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11  

1 2 1  A    
Fetus
and adult
Embryo
Embryo
Fetus
Adult
The human a-globin and b-globin gene families

69. 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

70. 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

71. 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

72. LE 19-18 Gene Transposable element Nonsister chromatids Crossover
Incorrect pairing
of two homologues
during meiosis
and

73. 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

74. LE 19-19 Evolutionary time Ancestral globin gene Duplication of
ancestral gene
Mutation in
both copies  
Transposition
to different
chromosomes
Evolutionary time  
Further
duplications
and mutations       

1 2 1    A   
a-Globin gene family
on chromosome 16
-Globin gene family
on chromosome 11

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

76. The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation

78. 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

79. 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

80. LE 19-20
EGF
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons (green)
Exon
shuffling
Exon
duplication F F F F
Fibronectin gene with multiple
“finger” exons (orange) F
EGF K K K
Plasminogen gene with a
“kringle” exon (blue)
Exon
shuffling
Portions of ancestral genes
TPA gene as it exists today

81. 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