2. Genome Anatomies
2.1. An Overview of Genome Anatomies
2.2. The Anatomy of the Eukaryotic Genome
2.3. The Anatomy of the Prokaryotic Genome
2.4. The Repetitive DNA Content of Genomes
LEARNING OUTCOME
When you have read Chapter 2, you should be able to:
1. Draw diagrams illustrating the major differences between the genetic organizations of the
genomes of humans, plants, insects, yeast and bacteria, and give an explanation for the C-value
paradox
2. Describe the DNA-protein interactions that give rise to the chromatosome and the 30 nm
chromatin fiber
3. State the functions of centromeres and telomeres and list their special structural features
4. Explain why chromosome banding patterns and the isochore model suggest that genes are not
evenly distributed in eukaryotic chromosomes
5. Outline the differences between the gene contents of different eukaryotic genomes and explain,
with examples, what is meant by ‘multigene family'
6. Describe the physical features and gene contents of mitochondrial and chloroplast genomes and
discuss the current hypothesis concerning the origins of organelle genomes
7. Describe the physical structure of the Escherichia coli genome and indicate the ways in which this
structure is and is not typical of other prokaryotes
8. Define, with examples, the term ‘operon'
9. Explain why prokaryotic genome sequences have complicated the species concept
10. Speculate on the content of the minimal prokaryotic genome and on the identity of
distinctiveness genes
11. Define the term ‘satellite DNA' and distinguish between satellite, minisatellite and microsatellite
DNA
12. Give examples of the various types of RNA and DNA transposons, and outline their transposition
pathways
2.1. An Overview of Genome Anatomies
Figure 2.1. Cells of eukaryotes (left) and prokaryotes (right). The top part of the figure
shows a typical human cell and typical bacterium drawn to scale. The human cell is 10 μm
in diameter and the bacterium is rod-shaped with dimensions of 1 × 2 μm. The lower
drawings show the internal structures of eukaryotic and prokaryotic cells. Eukaryotic cells
are characterized by their membrane-bound compartments, which are absent from
prokaryotes. The bacterial DNA is contained in the structure called the nucleoid.
Figure 2.2. Comparison of the genomes of humans, yeast, fruit flies, maize and Escherichia coli. (A) is the 50-kb
segment of the human β T-cell receptor locus shown in Figure 1.14 . This is compared with 50-kb segments from the
genomes of (B) Saccharomycescerevisiae (chromosome III; redrawn from Oliver et al., 1992); (C) Drosophila
melanogaster (redrawn from Adams et al., 2000); (D) maize (redrawn from SanMiguel et al., 1996) and (E) E. coli K12
(redrawn from Blattner et al., 1997). See the text for more details.
Figure 2.3. Plasmids are small circular DNA molecules that are found inside some
prokaryotic cells.
2.2. The Anatomy of the Eukaryotic Genome
Figure 2.4. Nuclease protection analysis of chromatin from human nuclei. Chromatin is gently
purified from nuclei and treated with a nuclease enzyme. On the left, the nuclease treatment is
carried out under limiting conditions so that the DNA is cut, on average, just once in each of the
linker regions between the bound proteins. After removal of the protein, the DNA fragments are
analyzed by agarose gel electrophoresis (see Technical Note 2.1) and found to be 200 bp in length,
or multiples thereof. On the right, the nuclease treatment proceeds to completion, so all the DNA in
the linker regions is digested. The remaining DNA fragments are all 146 bp in length. The results
show that in this form of chromatin, protein complexes are spaced along the DNA at regular
intervals, one for each 200 bp, with 146 bp of DNA closely attached to each protein complex.
Figure 2.5. Nucleosomes. (A) Electron micrograph of a purified chromatin strand showing
the ‘beads-on-a-string' structure. (Courtesy of Dr Barbara Hamkalo, University of
California, Irvine.) (B) The model for the ‘beads-on-a-string' structure in which each bead
is a barrel-shaped nucleosome with the DNA wound twice around the outside. Each
nucleosome is made up of eight proteins: a central tetramer of two histone H3 and two
histone H4 subunits, plus a pair of H2A-H2B dimers, one above and one below the central
tetramer (see Figure 8.9 ). (C) The precise position of the linker histone relative to the
nucleosome is not known but, as shown here, the linker histone may act as a clamp,
preventing the DNA from detaching from the outside of the nucleosome.
Figure 2.6. The solenoid model for the 30 nm chromatin fiber. In this model, the ‘beads-ona-string' structure of chromatin is condensed by winding the nucleosomes into a helix with
six nucleosomes per turn. Higher levels of chromatin packaging are described in Section
8.1.2.
Figure 2.7. The typical appearance of a metaphase chromosome. Metaphase chromosomes
are formed after DNA replication has taken place, so each one is, in effect, two
chromosomes linked together at the centromere. The arms are called the chromatids. A
telomere is the extreme end of a chromatid
Figure 2.8. The human karyogram.
The chromosomes are shown with
the G-banding pattern obtained
after Giemsa staining.
Chromosome numbers are given
below each structure and the band
numbers to the left. ‘rDNA' is a
region containing a cluster of
repeat units for the ribosomal RNA
genes, which specify a type of noncoding RNA (Section 3.2.1).
‘Constitutive heterochromatin' is
very compact chromatin which has
few or no genes (Section 8.1.2).
Redrawn from Strachan and Read
(1999).
Figure 2.9. The role of the kinetochores during nuclear division. During the anaphase
period of nuclear division (see Figures 5.14 and 5.15 ), individual chromosomes are
drawn apart by the contraction of microtubules attached to the kinetochores.
Figure 2.10. Telomeres. The sequence at the end of a human telomere. The length of
the 3′ extension is different in each telomere. See Section 13.2.4 for more details about
telomeric DNA
Figure 2.11. Gene density along the largest of the five Arabidopsis thaliana
chromosomes. Chromosome 1, which is 29.1 Mb in length, is illustrated with the
sequenced portions shown in red and the centromere and telomeres in blue. The
gene map below the chromosome gives gene density in pseudocolor, from deep
blue (low density) to red (high density). The density varies from 1 to 38 genes per
100 kb. Reprinted with permission from AGI (The Arabidopsis Genome Initiative),
Nature, 408, 797–815. Copyright 2000 Macmillan Magazines Limited.
Figure 2.12. Comparison of the gene catalogs of Saccharomyces cerevisiae, Arabidopsis
thaliana, Caenorhabditis elegans, fruit fly and humans. Genes are categorized according
to their function, as deduced from the protein domains specified by each gene.
Redrawn from IHGSC (2001)
Figure 2.13. Relationship between the human gene catalog and the catalogs of other
groups of organism. The pie chart categorizes the human gene catalog according to the
distribution of individual genes in other organisms. The chart shows, for example, that
22% of the human gene catalog is made up of genes that are specific to vertebrates, and
that another 24% comprises genes specific to vertebrates and other animals. Genes are
categorized according to their function, as deduced from the protein domains specified by
each gene. Redrawn from IHGSC (2001).
Figure 2.14. The human α- and β-globin gene clusters. The α-globin cluster is located on
chromosome 16 and the β-cluster on chromosome 11. Both clusters contain genes that are
expressed at different developmental stages and each includes at least one pseudogene.
Note that expression of the α-type gene ξ2 begins in the embryo and continues during the
fetal stage; there is no fetal-specific α-type globin. The θ pseudogene is expressed but its
protein product is inactive. None of the other pseudogenes is expressed. For more
information on the developmental regulation of the β-globin genes, see Section 8.1.2.
Figure 2.15. The Saccharomyces cerevisiae mitochondrial genome. Because of their relatively small
sizes, many mitochondrial genomes have been completely sequenced. In the yeast genome, the genes
are more spaced out than in the human mitochondrial genome ( Figure 1.22 ) and some of the genes
have introns. This type of organization is typical of many lower eukaryotes and plants. The yeast
genome contains five additional open reading frames (not shown on this map) that have not yet been
shown to code for functional gene products, and there are also several genes located within the
introns of the discontinuous genes. Most of the latter code for maturase proteins involved in splicing
the introns from the transcripts of these genes (Section 10.2.3). Abbreviations: ATP6, ATP8, ATP9,
genes for ATPase subunits 6, 8 and 9, respectively; COI, COII, COIII, genes for cytochrome c oxidase
subunits I, II and III, respectively; Cytb, gene for apocytochrome b; var 1, gene for a ribosomeassociated protein. Ribosomal RNA and transfer RNA are two types of non-coding RNA (Section 3.2.1).
The 9S RNA gene specifies the RNA component of the enzyme ribonuclease P (Section 10.2.2).
Figure 2.16. The rice chloroplast
genome. Only those genes with
known functions are shown. A
number of the genes contain introns
which are not indicated on this map.
These discontinuous genes include
several of those for tRNAs, which is
why the tRNA genes are of different
lengths even though the tRNAs that
they specify are all of similar size
2.3. The Anatomy of the Prokaryotic Genome
Figure 2.17. Supercoiling. The diagram shows how underwinding a circular doublestranded DNA molecule results in negative supercoiling
Figure 2.18. A model for the structure of the Escherichia coli nucleoid. Between 40 and 50
supercoiled loops of DNA radiate from the central protein core. One of the loops is shown
in circular form, indicating that a break has occurred in this segment of DNA, resulting in
a loss of the supercoiling
Figure 2.19. The genome of Escherichia coli K12. The map is shown with the origin of
replication (Section 13.2.1) positioned at the top. Genes on the outside of the circle
are transcribed in the clockwise direction and those on the inside are transcribed in
the anticlockwise direction. Image supplied courtesy of Dr FR Blattner, Laboratory of
Genetics, University of Wisconsin-Madison. Reproduced with permission
Figure 2.20. Two operons of Escherichia
coli. (A) The lactose operon. The three
genes are called lacZ, lacY and lacA, the
first two separated by 52 bp and the
second two by 64 bp. All three genes are
expressed together, lacY coding for the
lactose permease which transports
lactose into the cell, and lacZ and lacA
coding for enzymes that split lactose into
its component sugars - galactose and
glucose. (B) The tryptophan operon,
which contains five genes coding for
enzymes involved in the multistep
biochemical pathway that converts
chorismic acid into the amino acid
tryptophan. The genes in the tryptophan
operon are closer together than those in
the lactose operon: trpE and trpD
overlap by 1 bp, as do trpB and trpA;
trpD and trpC are separated by 4 bp, and
trpC and trpB by 12 bp. For more details
on the regulation of these operons, see
Sections 9.3.1 and 12.1.1
Figure 2.21. A typical operon in the genome of Aquifex aeolicus. The genes code for the
following proteins: gatC, glutamyl-tRNA aminotransferase subunit C, which plays a role in
protein synthesis (Section 11.2); recA, recombination protein RecA; pilU, twitching mobility
protein; cmk, cytidylate kinase, required for synthesis of cytidine nucleotides; pgsA,
phosphotidylglycerophosphate synthase, an enzyme involved in lipid biosynthesis; recJ,
single-strand-specific endonuclease RecJ, which is another recombination protein (Section
14.3).
Figure 2.22. The impact of lateral gene transfer on the content of prokaryotic genomes.
The chart shows the DNA that is unique to a particular species in blue and the DNA that
has been acquired by lateral gene transfer in red. The number at the end of each bar
indicates the percentage of the genome that derives from lateral transfer. Note that
intergenic regions are omitted from this analysis. Redrawn from Ochman et al. (2000)
Figure 2.23. Lateral gene transfer obscures the
evolutionary relationships between species. In (A) a
group of eight modern species has evolved from an
ancestor without lateral gene transfer. The evolutionary
relationships between the species can be inferred by
comparisons between their DNA sequences, using the
molecular phylogenetics techniques described in
Chapter 16. In (B) extensive lateral gene transfer has
occurred. The evolutionary histories of the modern
species cannot now be inferred by standard molecular
phylogenetics because one or more of the species may
have acquired the sequences that are being compared
by lateral gene transfer rather than by inheritance from
a direct ancestor
Figure 2.24. Satellite DNA from the human genome. Human DNA has an average GC
content of 40.3% and average buoyant density of 1.701 g cm-3. Fragments made up mainly
of single-copy DNA have a GC content close to this average and are contained in the main
band in the density gradient. The satellite bands at 1.687, 1.693 and 1.697 g cm-3 consist
of fragments containing repetitive DNA. The GC contents of these fragments depend on
their repeat motif sequences and are different from the genome average, meaning that
these fragments have different buoyant densities to single-copy DNA and migrate to
different positions in the density gradient.
2.4. The Repetitive DNA Content of Genomes
Figure 2.25. The use of microsatellite analysis in genetic profiling. In this example,
microsatellites located on the short arm of chromosome 6 have been amplified by the
polymerase chain reaction (PCR; Section 4.3). The PCR products are labeled with a blue
or green fluorescent marker and run in a polyacrylamide gel (see Technical Note 6.1),
each lane showing the genetic profile of a different individual. No two individuals have
the same genetic profile because each person has a different set of microsatellite
length variants, the variants giving rise to bands of different sizes after PCR. The red
bands are DNA size markers. Image supplied courtesy of PE Biosystems, Warrington,
UK, and reproduced with permission.
Figure 2.26. Retrotransposition. Compare with Figure 1.19 (page 22), and note that the
events are essentially the same as those that result in a processed pseudogene.
Figure 2.27. Retroelements. A comparison of the structures of four types of retroelement.
Retroviruses and retrotransposons are LTR elements that possess long terminal repeats at
each end. The gag gene codes for a series of proteins located in the virus core; pol codes
for the reverse transcriptase and other enzymes involved in replication of the element;
env codes for coat proteins. LINEs and SINEs are non-LTR retroelements or retroposons.
Both have a poly(A) region (a long series of A nucleotides) at one end.
Figure 2.28. Two mechanisms of transposition used by DNA transposons. For more
details see Section 14.3.3
Figure 2.29. DNA transposons of prokaryotes. Four types are shown. Insertion
sequences, Tn3-type transposons and transposable phages are flanked by short (< 50 bp)
inverted terminal repeat (ITR) sequences. The resolvase gene of the Tn3-type transposon
codes for a protein involved in the transposition process.