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Levels at which Eucaryote Genome
Organization can be Studied
Linear
Sequence
Gene organization/
organization of
‘non-gene’
sequences
…ATAGC...
Repetitive
Element
Gene
Pseudogene
Banding
Patterns/
Chromatin
Structure
DNA Content of Haploid Genomes
of a Range of Phyla
Flowering plants
Birds
Mammals
Reptiles
Amphibians
Bony fish
Cartilaginous fish
Echinoderms
Crustaceans
Insects
Molluscs
Worms
Fungi
Algae
Bacteria
Mycoplasmas
Viruses
(Plasmids)
103
105
10 7
109
DNA content (bp)
1011
Eucaryote Chromosome Numbers
Organism
Common
Diploid Chromosome
Name
Number
_____________________________________________________
Myrmecia pilosula
Ant
2
Felis catus
Cat
38
Homo sapiens
Human
46
Canis familiaris
Dog
78
Ophioglossum reticulatum
Fern
1260
Human Chromosome Sizes
Size (Mb)
Chromosome
Number
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
X
Y
50
100
150
200
250
Eucaryote Genome Sizes
• Eucaryote genome size 100-100000 times larger
than bacterial chromosome
• Why do eucaryotes have larger genomes?
Developmental and differentiation processes
• Larger genome size  greater complexity (cf.
bacteria)
• Repetitive sequences
Proportions of Repetitive and
Nonrepetitive DNA in Example Genomes
1010
64
Genome size (bp)
109
70
36
54 46
30
30
108
70
83
17
107
100
106
105
Nonrepetitive
DNA
Repetitive
DNA
Human Genome Organization
HUMAN GENOME
Nuclear genome
3000 Mb
30-40000 genes?
~30%
Mitochondrial genome
16.6 kb
37 genes
~70%
Genes and generelated sequences
Extragenic
DNA
Unique or moderately repetitive
~10%
~90%
Coding
DNA
Pseudogenes
Noncoding
DNA
Gene
fragments
Introns,
untranslated
sequences, etc.
Two rRNA
genes
22 tRNA
genes
13 polypeptideencoding genes
80%
20%
Unique or
low copy
number
Moderate to
highly
repetitive
Tandemly
repeated
or clustered
repeats
Interspersed
repeats
How Many Genes in the Human Genome?
• Current estimate is 30,000-40,000
Drosophila (fruitfly) has ~13,000 genes
C. elegans (nematode worm) has ~20,000 genes
Mouse has ~30,000 genes
• Human gene transcripts (mRNA) commonly undergo
alternative splicing
Exon
DNA
Transcription
Intron
pre-mRNA
Splicing
mRNA1
Translated into
3 proteins
mRNA2
mRNA3
• More human genes are transcription factors which
interact with larger number of control elements
Types of Repetitive Sequence in the
Human Genome
• Tandem repeats: satellite DNA
• Interspersed repeats
SINEs, e.g., Alu elements
Retroviral-like sequences. e.g., LINEs
• Duplicated genes incl. pseudogenes
Satellite DNA
[DNA]
Main band
Satellite band
Density
• Tandem repeats 1-170 bp in length
• Can total several Mb in length
• Noncoding/nontranscribed
• May have a structural role?
• ~10-20% of human genome
Satellite DNA Amplification
Amplification
Mutation
New amplification unit
Amplification
Short Interspersed Repetitive Elements
(SINEs): Alu Elements
Characteristics
• Consensus: 281 nt
• Consists of two related units
• Considerable variation in length due to deletions,
substitutions, or insertions
• ~1,000,000 elements/haploid genome (~12%)
Distribution
• Average spacing is 4-kb apart
• Scattered but non-random?
• Deleterious when inserted within a gene
• Examples of insertions which assist in
transcription regulation when inserted in control
region of a gene
• Selfish DNA?
1
41
81
121
161
201
241
281
GGCCGGGCGC
GGGAGGCCGA
GACCATCCCG
AAATACAAAA
AGTCCCAGCT
GAACCCGGGA
CACTGCACTC
C
GGTGGCTCAC
GGCGGGCGGA
GCTAAAACGG
AATTAGCCGG
ACTTGGGAGG
GGCGGAGCTT
CAGCCTGGGC
GCCTGTAATC
TCACGAGGTC
TGAAACCCCG
GCGTAGTGGC
CTGAGGCAGG
GCAGTGAGCC
GACAGAGCGA
CCAGCACTTT
AGGAGATCGA
TCTCTACTAA
GGGCGCCTGT
AGAATGGCGT
GAGATCCCGC
GACTCCGTCT
Long Interspersed Nuclear Elements (LINEs)
Characteristics
• 60 bp - 7 kb
• Considerable variation in length due to
5’ truncations, deletions, and rearrangements
• ~500,000 elements/haploid genome (15-20%)
• 3-4,000 are full-length
• 1-2% capable of transposition, probably via an
RNA intermediate (as with retroviruses)
Distribution
• Found in A-T rich regions
5’
3’
ORF2
ORF1
A-T
rich
Pseudogenes and Gene Fragments
• Many eucaryotic genes exist as variants which,
for example, may be expressed during different
stages of development
• Families of evolutionarily-diverged genes with
related functions
• Pseudogenes:
• Nonfunctional gene copies or gene fragments
which have arisen during gene family
expansion
• Contain insertions, deletions, nonsense
mutations
• Usually non-transcribed
• May be associated with functional gene copy
-globin Region on Human Chromosome 11

2
1
G

A

10 kb
Alu repeats
LINEs
Splicing Removes Introns from a Primary
Transcript
Exon
DNA
Transcription
pre-mRNA
Splicing
mRNA
Translation
Protein
Intron
Intron Numbers in Selected Human Genes
Gene
Size (kb)
Number of introns
_______________________________________________
Thrombomodulin
3.7
0
-globin
1.4
2
Ovalbumin
7.7
7
BRCA1
100
22
von Willebrand factor
175
52
2400*
79
Dystrophin
*The size of a bacterial genome!
Introns in Globin Gene Family
Gene
Size
(bp)
Plant globin
1098
Leghaemoglobin
876
Myoglobin
8659
Human -globin
677
Human -globin
1418
50
100
Number of amino acids
150
Summary
• Eucaryotic genome sizes > bacterial genome
sizes
• Different chromosome numbers and genome
sizes in eucaryotes, but not absolutely
correlated with evolutionary position
• ~3% of human genome is coding
• Remainder is extragenic or noncoding
(pseudogenes, introns, etc.)
• Repetitive DNA constitutes a large part of human
genome:
 Tandem repeats: satellite DNA
 Interspersed repeats: SINEs, LINEs
 Duplicated genes: pseudogenes
• Introns