Genomes

1
Genomes

• Chapter 21

2
Genomes

• Sequencing of DNA
• Human Genome Project
• 1990-2003
• 6 countries
• 20 research centers

3
Genome

• J. Craig Venter in 1992
• Whole-genome shotgun approach
• Sequences random DNA fragments directly

4
Fig. 21-3-3
1
Cut the DNA into overlapping fragments short
enough for sequencing
2
Clone the fragments in plasmid or phage vectors.
3
Sequence each fragment.
4
Order the sequences into one overall sequence with
computer software.
5
Genomes

• Complete genome sequences
• Human, chimpanzee,
• E. coli, brewers yeast
• Nematode, fruit fly, house mouse,

6
Genomes

• Genomics
• Study of whole sets of genes their interactions
• Bioinformatics
• Application of computers
• Storage Analysis of biological data

7
Genomes

• Metagenomics
• DNA
• Entire groups of species
• Environmental sample
• Sequenced
• Human microbiome

8
Figure 21.1
9
Genomes

• Comparison
• Evolutionary history of genes
• Taxonomic groups

10
Genome

• Phenotype to genotype
• Red eye fruit flies (ww or ww)
• Computer analysis of genome
• Identifies sequences likely to encode proteins
• Genotype to phenotype

11
Genomes
12
Genome

• NCBI
• Genbank
• BLAST
• Compare DNA Sequences
• Compare predicted protein sequences
• Domains (known aa sequences)

13
Fig. 21-4
14
tatggagaga ataaaagaac tgagagatct aatgtcgcag
tcccgcactc gcgagatact 61 cactaagacc actgtggacc
atatggccat aatcaaaaag tacacatcag gaaggcaaga 121
gaagaacccc gcactcagaa tgaagtggat gatggcaatg
agatacccaa ttacagcaga 181 caagagaata atggacatga
ttccagagag gaatgaacaa gggcaaaccc tctggagcaa 241
aacaaacgat gctggatcag accgagtgat ggtatcacct
ctggccgtaa catggtggaa 301 taggaatggc ccaacaacaa
gtacagttca ttaccctaag gtatataaaa cttatttcga 361
aaaggtcgaa aggttgaaat atggtacctt cggccctgtc
cacttcagaa atcaagttaa 421 aataaggagg agagttgata
caaaccctgg ccatgcagat ctcagtgcca aggaggcaca 481
ggatgtgatt atggaagttg ttttcccaaa tgaagtgggg
gcaagaatac tgacatcaga 541 gtcacagctg gcaataacaa
aagagaagaa agaagagctc caggattgta aaattgctcc 601
cttgatggtg gcgtacatgc tagaaagaga attggtccgt
aaaacaaggt ttctcccagt 661 agccggcgga acaggcagtg
tttatattga agtgttgcac ttaacccaag ggacgtgctg 721
ggagcagatg tacactccag gaggagaagt gagaaatgat
gatgttgacc aaagtttgat 781 tatcgctgct agaaacatag
taagaagagc agcagtgtca gcagacccat tagcatctct 841
cttggaaatg tgccacagca cacagattgg aggagtaagg
atggtggaca tccttagaca 901 gaatccaact gaggaacaag
ccgtagacat atgcaaggca gcaatagggt tgaggattag 961
ctcatctttc agttttggtg ggttcacttt caaaaggaca
agcggatcat cagtcaagaa
15
Genome

• Proteomics
• Systematic study of all proteins encoded by a
  genome
• Proteins carry out most of the cells activities

16
Application

• Finding DNA sequence of organisms
• Predict structure function of new proteins
  RNA sequences
• Families of related proteins
• Phylogenic trees evolutionary relationships

17
Application

• The Cancer Genome Atlas project
• Monitors 2,000 genes in cancer cells for changes
• Mutations rearrangements
• Lung, ovarian and glioblastoma
• Compare to normal cells

18
Application

• DNA sequencing
• Highlight diseases
• Specialize tx

19
Genome size

• Bacteria range from 1 to 6 million base pairs
  (Mb)
• Eukaryotes usually larger
• Humans have 3,200 Mb

20
Table 21-1
21
Fig. 21-UN1
Bacteria
Archaea
Eukarya
Genome size
Most are 104,000 Mb, but a few are much larger
Most are 16 Mb
Number of genes
1,5007,500
5,00040,000
Gene density
Lower than in prokaryotes (Within eukaryotes,
lower density is correlated with larger genomes.)
Higher than in eukaryotes
None in protein-coding genes
Present in some genes
Unicellular eukaryotes present, but prevalent
only in some species Multicellular
eukaryotes present in most genes
Introns
Other noncoding DNA
Can be large amounts generally more
repetitive noncoding DNA in multicellular
eukaryotes
Very little
22
Genome

• Gene density
• Number of genes in a given length of DNA
• Humans other mammals-lowest
• Multicellular eukaryotes have many introns
• Junk DNA

23
Genome

• Genomes of humans, rats, mice
• 500 noncoding regions-are the same
• 98.5 of the genome does not code for proteins,
  rRNAs, or tRNAs
• 24 regulatory sequences introns

24
Fig. 21-7
Exons (regions of genes coding for protein or
giving rise to rRNA or tRNA) (1.5)
Repetitive DNA that includes transposable elements
and related sequences (44)
Introns and regulatory sequences (24)
Unique noncoding DNA (15)
L1 sequences (17)
Repetitive DNA unrelated to transposable elements
(15)
Alu elements (10)
Simple sequence DNA (3)
Large-segment duplications (56)
25
Genome

• Pseudogene
• Former genes, mutated
• Repetitive genes
• Sequences in multiple copies

26
Genome

• Transposable elements
• DNA that move from one site to another
• Prokaryotes eukaryotes
• Barbara McClintock

27
Fig. 21-8
28
Genome

• Eukaryotic transposable elements
• 1. Transposons
• Move within a genome
• DNA intermediate
• 2. Retrotransposons
• Move - RNA intermediate

29
Fig. 21-9a
New copy of transposon
Transposon
DNA of genome
Transposon is copied
Insertion
Mobile transposon
(a) Transposon movement (copy-and-paste
mechanism)
30
Fig. 21-9b
New copy of retrotransposon
Retrotransposon
RNA
Insertion
Reverse transcriptase
(b) Retrotransposon movement
31
Genome

• Alu elements
• 10 of genome
• Transposable elements
• 300 nucleotides
• Do not code for protein
• Code for RNA

32
Genome

• Line-1 or L1
• 17 genome
• Retrotransposons
• 6500 nucleotides
• Low transposition
• Regulate gene expression
• Developing neurons

33
Genome

• Repetitive DNA not transposons
• 15
• 1. Long sequences of DNA
• 2. Simple sequence DNA
• Many copies of repeated short sequences
• GTTACGTTACGTTACGTTACGTTAC

34
Genome

• Short tandem repeat (STR)
• Repeating units of 2 to 5 nucleotides
• Vary among individuals
• Centromeres
• Telomeres

35
Genome

• Multigene families
• Collections of identical or very similar genes on
  a haploid set of chromosomes
• Example
• Code for rRNA products
• Single transcript makes all rRNA molecules
• Transcript sequence repeated many times

36
Fig. 21-10a
DNA
RNA transcripts
Nontranscribed spacer
Transcription unit
DNA
28S
18S
5.8S
rRNA
5.8S
28S
18S
(a) Part of the ribosomal RNA gene family
37
Genome

• Nonidentical genes
• Hemoglobin
• Chromosome 16-a globulin
• Chromosome 11-ß globulin
• Code separately
• Animal development

38
Fig. 21-10b
Heme
?-Globin
Hemoglobin
?-Globin
?-Globin gene family
?-Globin gene family
Chromosome 16
Chromosome 11
?
?
?
G?
A?
?
?2
??1
?1
??2
??
??
??
Fetus and adult
Embryo
Embryo
Fetus
Adult
(b) The human ?-globin and ?-globin gene families
39
Evolution

• Human chimpanzee genomes differ by 1.2
• More Alu elements in humans
• Several genes are evolving faster in humans
• Genes involved in defense against malaria and
  tuberculosis
• Gene that regulations brain size
• Genes that code for transcription factors

40
Fig. 21-15
Bacteria
Most recent common ancestor of all living things
Eukarya
Archaea
4
3
2
1
0
Billions of years ago
Chimpanzee
Human
Mouse
70
0
10
20
30
40
50
60
Millions of years ago
41
Evolution

• FOXP2 gene
• Vocalization
• Mutation causes speech impairment
• 2 aa difference chimps and humans

42
Evolution

• Humans 23 pairs of chromosomes
• Chimpanzees 24 pairs
• Humans chimpanzees diverged from a common
  ancestor
• 2 ancestral chromosomes fused in humans
• Duplications inversions result from mistakes
  during meiotic recombination

43
Figure 21.11
Chimpanzeechromosomes
Humanchromosome
Telomeresequences
Centromeresequences
Telomere-likesequences
12
Centromere-likesequences
2
13
44
Figure 21.12
Human chromosome
Mouse chromosomes
16
17
16
7
8
45
Figure 21.14
Ancestral globin gene
Duplication ofancestral gene
Mutation inboth copies
ß
a
Transposition todifferent chromosomes
Evolutionary time
a
ß
Further duplicationsand mutations
?
ß
?
a
?
?ß
?
A?
a2
a1
??
y?
?
ß
G?
?
a-Globin gene familyon chromosome 16
ß-Globin gene familyon chromosome 11
46
Figure 21.16
EGF
EGF
EGF
EGF
Epidermal growthfactor gene with multipleEGF
exons
Exonshuffling
Exonduplication
F
F
F
F
Fibronectin gene with multiplefinger exons
EGF
F
K
K
K
Exonshuffling
Plasminogen gene with akringle exon
Portions of ancestral genes
TPA gene as it exists today
47
Evolution

• Evo-devo
• Evolutionary developmental biology
• Developmental processes in multicellular
  organisms
• Genomic information shows minor differences in
  gene sequence or regulation
• Results in major differences in form

48
Evolution

• Homeotic genes
• Body segments (fruit fly)
• 180-nucleotide sequence
• Homeobox
• Related homeobox sequences have been found in
  regulatory genes of yeasts, plants, and even
  eukaryotes

49
Fig. 21-17
Adult fruit fly
Fruit fly embryo (10 hours)
Fly chromosome
Mouse chromosomes
Mouse embryo (12 days)
Adult mouse