Hillary Term 04: “The Human Genome”
20.1 The Human Genome – evolutionary issues (Hein)
27.1 Non-Genic Selection in the Human Genome (Lunter)
3.2 Mammalian Genes I: Conservation and slow evolution (Ponting)
10.2 Mammalian Genes II: Functional innovation and rapid change (Ponting/Goodstadt)
17.2 RNAs in Human Genome (Sam Griffiths-Jones)
24.2 Population Genetics of the Human Genome (Gil McVean )
2.3 Association Mapping and the Human Genome (Lon Cardon)
9.3 The Human Genome and Human Evolution (Chris Tyler-Smith)
The Human Genome – key issues
The Human Genome Project
Few basic facts of the human genome
Grammar of Genes
Basic events happening to a genome per mitosis/generation
Genealogical Structures: Phylogenies, Pedigrees and the ARG
Long term Dynamics of the Human Genome: The comparative aspect
(Genotype  Phenotype) & (Population Genetics/History) => Gene Mapping
History
Our interests.
History of the Human Genome Project
1956 Physical map. 24 types and total set of 46 chromosomes
1977 Sanger publishes dideoxy sequencing method
1980 Botstein proposes human genetic map using RFLPs
1987 US DOE publishes report discussing HGP
1988 HUGO is established
1990 Official start of HGP with 3 billion $ and a 15 year horizon.
1991 Genome Database GB is established
1992 Genethon publishes map based on microsatelites.
1995 Lander et al. detailed map based on sequence tagged sites.
1998 Comprehensive map based on gene markers.
1999 Sanger Centre publishes chromosome 22
2001 Draft Genome published: Celera & Public
2003 Completion (almost) of Human Genome
Strachan and Read, HMG3 p213
Sequencing Strategies
Public effort- strategy:
Celera’s view of International Consortium
Unfair competition: IC delivering the
same goods but with state funding.
Celera - strategy:
From Myers 99
International Consortium’s view of Celera
Unfair competition: Celera delivering the
same goods but can use IC data, while
IC cannot use Celera data.
Other Genome Projects
1976/79 First viral genome – MS2/fX174
1980
Mitochondrion
1982
First shotgun sequenced genome – Bacteriophage lambda
1995
First prokaryotic genome – H. influenzae
1996
First unicellular eukaryotic genome – Yeast
1998
The first multicellular eukaryotic genome – C.elegans
2000
Drosophila melanogaster
2000
Arabidopsis thaliana
2001
Human Genome
2002
Mouse Genome
The Genome OnLine Database knows of 958 genome sequencing projects,
of which 169 are completed
Favourite and Model Organisms
Multicellular Animals
Mammals
Human
Mouse
Cow
Dog
Rat
Chimp
Pig
3.5
3.2
3.0
2.8
3.1
3.5
3.0
Fish
Puffer Fish
Zebra Fish
0.4 Gb
1.9 Gb
Insects
Drosophila
Honey Bee
Yellow Fever Mosquito
Malaria Mosquito
Strachan and Read (2004) Chapter 8
Gb
Gb
Gb
Gb
Gb
Gb
Gb
Birds
Chicken
1.2 Gb
Frog
Xenopus Laevis
1.7 Gb
Nematodes
Caenorhabdites elegans 100 Mb
Caenorhabdites briggsae 80 Mb
Sea Urchin
Strongylocentrotus purpuratus
Multicellular Plants
165
270
780
278
Mb
Mb
Mb
Mb
Arabidopsis thaliana
Rice
125 Mb
430 Mb
800 Mb
The Human Genome I
1
2
3
http://www.sanger.ac.uk/HGP/ & R.Harding & HMG (2004) p 245
4
5
6
7
8
9
10
11
12
13 14
16
15
104
279
221
251
17
18
19 20
72
88
Y
.016
45 48
51
Myoglobin
*5.000
*20
Exon 3
3’ flanking
ATTGCCATGTCGATAATTGGACTATTTGGA
aa
3.2*109 bp
6*104 bp
5’ flanking
aa
mitochondria
b-globin
Exon 1 Exon 2
Protein:
22
163
a globin
(chromosome 11)
DNA:
21
86
118 107 100
148
143
142
176 163 148 140
197 198
66
X
aa
aa
aa
aa
aa
aa
aa
aa
3*103 bp
*103
30 bp
The Human Genome II
http://www.sanger.ac.uk/HGP/
Highly conserved - coding
Highly conserved - other
Transposon based repeats
Heterochromatin
Other non-conserved
Gene Density:
Pseudogenes:
Nuclear Genome
1.5%
3.5%
45 %
6.6%
44 %
Mendelian inheritance
1 (typically)
Recombination
1/130 kb
20000
Processed Pseudogenes
Strachan and Read (2004) Chapter 9
Mitochondria
93%
5%
2%
Maternal inheritance
Possibly thousands
No recombination
2 kb
The Human Genome III
http://www.sanger.ac.uk/HGP/
Gene families
Clustered
a-globins (7), growth hormone (5), Class I HLA heavy chain (20),….
Dispersed
Pyruvate dehydrogenase (2), Aldolase (5), PAX (>12),..
Clustered and Dispersed
HOX (38 – 4), Histones (61 – 2), Olfactory receptors (>900 – 25),…
Transposons
Strachan and Read (2004) Chapter 9 + Lander et al.(2001)
Genes and Gene Structures I
•Presently estimated Gene Number: 24.000 (reference: )
•Average Gene Size: 27 kb
•The largest gene: Dystrophin 2.4 Mb - 0.6% coding – 16 hours to transcribe.
•The shortest gene: tRNATYR 100% coding
•Largest exon:
ApoB exon 26 is 7.6 kb
Smallest: <10bp
•Average exon number: 9
•Largest exon number: Titin 363
Smallest: 1
•Largest intron: WWOX intron 8 is 800 kb
•Largest polypeptide: Titin 38.138
Smallest: 10s of bp
smallest: tens – small hormones.
•Intronless Genes: mitochondrial genes, many RNA genes, Interferons, Histones,..
Jobling, Hurles & Tyler-Smith (2004) HEG p 29 + HMG chapt. 9
Genes and Gene Structures II
Genes within Genes:
Intron 26 of neurofibromatosis type I (NF1) contains 3 internal (2 exons) genes in
the opposite direction.
Overlapping Genes:
Class III region of HLA
Strachan and Read (2004) Chapter 9 p 258
Simple Eukaryotic
Alternative Splicing
1. A challenge to automated annotation.
2. How widespread is it?
3. Is it always functional?
4. How does it evolve?
Cartegni,L. et al.(2002) “Listening to Silence and understanding nonsense: Exonic mutations that affect splicing” Nature Reviews Genetics 3.4.285HMG p291-294
RNAs in the Genome
~200
snoRNA
small nucleolar, over 100 types - RNA modification and processing
~100
snRNA
small nuclear - involved in splicing
~200
miRNA
very small ~22bp , regulation
~175
28S,5.8S,5S
large cytosolic subunit
~175
18S
small mitochondrial subunit
~250
5S
large mitochondrial subunit
>500
tRNA
>1500
Antisense RNA
Strachan and Read (2004) p.247 F9.4
transfer RNA
> 1500 types
Genome Annotation
Proteins
Genomes
ESTs
Ensembl
http://www.ensembl.org
Santa Cruz Genome Browser
http://genome.ucsc.edu/
Gene Finding and Protein (HMM) Descriptors
Burge & Karlin jmb 96
A. Make gene characteristics to each
nucleotide. Extract legal
prediction by dynamical
programming.
B. Use HMM to describe biological
knowledge of gene structure.
Mutations and Mutation Rates
1 mitosis or generation
Average Number of Mitoses
•
Single nucleotide substitutions: ~10-7
Male generation (15:35 .. 20:150
•
Microsatellites (~100.000): ~10-2
Female generation: ~24
•
Small insertion deletions: ~10-8
Crow,JF (2000) “The Origins, Patterns and Implications of Human Spontaneous Mutation” Nature Review Genetics 1.1.40-47 + Strachan and Read (2004) chapter 11 +Jobling, Hurles and TylerSmith (2004) chapter 2
Recombination
Recombination:
Gene Conversion:
1 meiosis
•Total Haploid length males: 25.9 M - females: 44.6 M.
•Gene conversions 1-2 orders higher. Length 300-2000 pb.
Lander et al.(2001) “Initial sequencing and analysis of the human genome” Nature 409.860-912. + Kong,E. et al.(2002) “A high resolution recombination map of the human genome” Nature Genetics
Selection: Positive & Negative
One sequence scenario
Population scenario
A
A
A
A
C
C
A
One sequence scenario again
ThrSer
ACGTCA
ThrPro
ACGCCA
A
A
A
A
A
A
A
C
C
A
A
A
C
C
The selection criteria could in principle
be anything, but the selection against
amino acid changes is without
comparison the most important.
ArgSer
AGGCCG
ThrSer
ACGCCG
ThrSer
ACTCTG
AlaSer
GCTCTG
AlaSer
GCACTG
Certain events have functional
consequences and will be selected
out. The strength and localization of
this selection is of great interest.
The Genetic Code
Substitutions
Number
Percent
Total in all codons
549
100
Synonymous
134
25
415
75
Missense
392
71
Nonsense
23
4
Nonsynonymous
Examples of rates
Organism
Gene
Syno/year
remade from Li,1997
Non-Syno/Year
RNA Virus
Influenza A
Hepatitis C
HIV 1
13.1 10-3
3.6 10-3
E
6.9 10-3
0.3 10-3
gag
2.8 10-3
1.7 10-3
P
4.6 10-5
1.5 10-5
Hemagglutinin
DNA virus
Hepatitis B
Genome
3.5 10-8
Mammals
c-mos
5.2 10-9
0.9 10-9
Mammals
a-globin
3.9 10-9
0.6 10-9
Mammals
histone 3
6.2 10-9
0.0
Herpes Simplex
Nuclear Genes
Genealogical Structures
ccagtcg
Homology:
The existence of a common ancestor
(for instance for 2 sequences)
Phylogeny
cagtct
ccggtcg
Pedigree:
Only finding common
ancestors. Only one
ancestor.
Ancestral Recombination Graph – the ARG
i. Finding common ancestors.
ii. A sequence encounters Recombinations
iii. A “point” ARG is a phylogeny
Populations
Grand parents
Parents
Now
Genealogical approach to Population Variation Analysis
Africa
Non-Africa
Inter.SNP Consortium (2001): A map of human genome
sequence variation containing 1.42 million SNPs. Nature 409.928-33
Pedigrees
Burke’s British Peerage
http://www.burkes-peerage.net/sites/wars/sitepages/home.asp
Chinese
Quebec French
http://demography.anu.edu.au/People/Staff/zhongwei.html
Heyer and Tremblay, 1998 PNAS
Mormons
http://genealogy-mormons.com/
Icelandic
http://www.decode.com + Helgason, A. et al. (2003 June) “A population-wide coalescent analysis of
Icelandic matrilineal and patrilineal genealogies: Evidence for a faster evolutionary rate of mtDNA
lineages than Y-chromosomes” American Journal Human Genetics.
Total Pedigree
Helga
son
1848
2
Ancestor cohort
1
1
1892
Year
2
2
3
1
2
1
2
1
1
1
1972
Contemporary cohort
2002
Matrilines
N = 31,817
Patrilines
Ancestral cohort
born 1848-1892
N = 31,659
73.9%
8.3%
3 .8
22.1%
g=
g=
4 .3
77.9%
91.7%
N = 64,150
26.1%
13.8%
86.2%
Descendant cohort
born after 1972
N = 66,910
Genealogical Questions
Pedigrees
Time back to first individual common ancestor to everyone
ARG questions:
The height of ARGs - correlation between local phylogenies
Gene Phylogeny Questions
Total Branch Length - Height
Long Term Evolutionary History: Myr/Gyr
Origin of Life
Last Universal Common Ancestor – LUCA
First Eukaryotes
First Chordates
First Vertebrates
First Mammals
First Primates
First Hominoids
Chimp-Human Split
Hedges, SB (2002) “The Origin and Evolution of Model Organisms” Nature Review Genetics 3.11.838-848.
Brown (2003) “Horizontal Genetic Transfers “ Nature Genetics
The Comparative Aspect.
MRCA-Most Recent Common Ancestor
Time Direction
3 Problems:
?
ATTGCGTATATAT….CAG
observable
ATTGCGTATATAT….CAG
observable
i. Test all possible relationships.
ii. Examine unknown internal states.
iii. Explore unknown paths between states at nodes.
ATTGCGTATATAT….CAG
observable
One Principle of Comparative Genomics
Observable
Unobservable
Protein Structure
Goldman, Thorne &
Jones, 96
P ( Sequence Structure) P ( Structure) 
C
RNA Structure
A
A
C
G
A
U
U
Gene Structure
Observable
C
Unobservable
P ( Structure Sequence ) P ( Sequence )
Molecular Evolution and Gene Finding: Two HMMs
AGTGGTACCATTTAATGCG.....
AGTGGTACTATTTAGTGCG.....
Simple Prokaryotic
Pcoding{ATG-->GTG} or
Pnon-coding{ATG-->GTG}
Simple Eukaryotic
The Rise of Comparative Genomics
Lander et al(2001) Figure 25A
The Domain of Comparative Genomics
Cabbage
ACTGT
Renin
1 2
ACTCCT
6
HIV proteinase
Sequences
RNA (Secondary) Structure
Protein Structure
3
5
4
1
6
5
7
8 2
7
3
8
4
Turnip
Gene Order/Orientation.
General Theme.
Formal Model of Structure
Stochastic Model of Structure Evolution.
Interaction Networks
Gene Structure
Any Graph.
Linkage Mapping
D
r
M
From McVean
Association/Fine scale mapping
Dominant/Recessive.
A set of characters.
Binary decision (0,1).
Spurious Occurrence
Quantitative Character.
Heterogeneity
genotype
Genotype  Phenotype
phenotype
2Ne generations
Penetrance
BRCA2 example
1000 cases and 1000 controls typed at 8 microsatellite markers
Single marker
association
Bayesian analysis
Causative SNPs.
Rafnar et al.(2004) – Morris et al(2001) +
Short Term Evolutionary History: Kyr/Myr
Oldest Polymorphisms
Supposedly well behaved populations
Neutral Human Autosomal Polymorphisms
Iceland
First Out-of-Africa
Finland
Anatomically Modern Man
Sardinia
Peopling of the Globe – genetic and fossil evidence.
The globe & migrations:
Cavalli-Sforza,2001 + HEG (2004)
Started October 27-29, 2002
“The International HapMap Project “Nature 426, 789 - 796 (18 Dec 2003)
HapMap
http://www.hapmap.org/
HapMap
Ontologies
A Structured Vocabulary – Consistent across species.
Purpose:
Facility communication among researchers
Facility communication among computer systems
Molecular Function
Biological Process
Cellular Component
http://www.geneontology.org
Gene Ontology Consortium (2001) “Creating the Gene Ontology Resource: Design and Implementation.” Genome Research 11.1425-33
Gene Ontology Consortium (2004) “The Gene Ontology (GO) database and informatics resource” Nucleic Acid Research 32.D258-61.
Source NAR(2004) 32.D258-
2001: Three Ontologies:
Structural Genomics: Systematic Structure Determination
Examples:
•Center for Eukaryotic Structural Genomics
•Structural Genomics of Pathogenic Protozoa Consortium
•Berkeley Structural Genomics Center : Mycoplasma genitalium and
Mycoplasma pneumoniae
PDB Holdings List: 10-Feb-2004
Molecule Type
Proteins,
Peptides, and
Viruses
Exp.
Tech.
X-ray Diffraction
and other
NMR
Total
http://www.strgen.org/
http://www.nysgrc.org/
http://www.oppf.ox.ac.uk/
Protein/Nucleic
Acid Complexes
Nucleic Acids
Carbohydrates
total
19014
898
719
14
20645
2934
96
569
4
3603
21948
994
1288
18
24248
http://pdb.ccdc.cam.ac.uk/pdb/strucgen.html
John Westbrook, Zukang Feng, Li Chen, Huanwang Yang and Helen M. Berman “The Protein Data Bank and structural genomics” Nucleic Acids Research, 2003, Vol. 31, No. 1 489-491
Structural Genomics: Mycoplasma pneumoniae proteins
http://www.strgen.org/status/mpoverview.html
Proteomics
2D PAGE gels (polyacryl gel electrophoresis )
MALDI
Source: Hanash (2003)
Protein Micro-arrays
Source Gavin et al.(2002)
http://www.hupo.org Hanash,S.(2003) “Disease Proteomics” Nature 422.226- Aebersold,R. and M.Mann (2003) “Mass spectrometry-based proteomics”
Nature 422.198- Gavin et al. (2002) “Functional Organisation of the Yeast Proteome by systematic analysis of protein complexes” Nature 415.141-
Summary
The Genome
Genomes: Variation and long term evolution.
Genealogical Structures: Phylogenies, Pedigrees and the ARG
Long term Dynamics of the Human Genome: The comparative aspect
(Genotype  Phenotype) & (Population Genetics/History) => Gene Mapping
Our Genomically Motivated Projects
1. Comparative gene annotation (Meyer, Skou Pedersen)
2. Superimposed selective constraints (Forsberg, Meyer, Skou
Pedersen) *
3. Haplotype Blocks (Song) *
4. Genome transformations (Miklos)
5. Ancestral Blocks*
6. Statistical Sequence Comparison (Drummond, Lunter, Miklos)
7. Substitutions and insertion-deletions at the Genome Level
(Lunter) Next week
Minimal ARGs and Haplotype Blocks (Song)
a: (3,4)
b: (3,4)
c: (15,16)
d: (16,17)
e: (35,36)
f: (35,36)
g: (36,37)
Combining Levels of Selection.
Forsberg, Meyer, Pedersen
Assume multiplicativity: fA,B = fA*fB
Protein-Protein
Hein & Støvlbæk, 1995
Codon Nucleotide Independence Heuristic
Jensen & Pedersen, 2001
Contagious Dependence
Protein-RNA
Singlet
Doublets
Contagious Dependence
Applications to Human Genome
Parameters used
Chromosome 1:
4Ne 20.000
Segments
(Wiuf and Hein,97)
Chromos. 1: 263 Mb.
52.000
263 cM
Ancestors
6.800
All chromosomes Ancestors
86.000
Physical Population. 1.3-5.0 Mill.
A randomly picked ancestor:
(ancestral material comes in batteries!)
0
260 Mb
0
52.000
*35
0
7.5 Mb
8360
6890
*250
0
30kb
References: Books & www-pages.
Books:
Strachan and Read (2004) “Human Molecular Genetics” (3rd Ed.) Bioscience
Jobling, Hurles and Tyler-Smith (2004) “Human Evolutionary Genetics” Bioscience
Sulston, J.(2002) “Our Common Thread” Corgi Books
Ridley, Matt (2001) “Genome”
“Encyclopedia of the Human Genome” (2003) Nature Publishing Group
Cavalli-Sforza,L. (2001) “Genes, People and Language” Penguin
Key articles:
Lander et al.(2001) “Initial Sequencing and Analysis of the Human Genome” Nature
Venter et al.(2001)”The Sequence of the Human Genome” Science 291.1304-1351
References: www-pages.
Major sequencing centers:
Baylor College of Medicine Genome Sequencing Center
hgsc.bcm.tcm.edu/
Celera
www.celera.com
DoE Joint Genome Institute
www.jgi.doe.gov
Genoscope
www.genoscope.cns.fr
TIGR
www.tigr.org
Washington University Genome Sequencing Center
www.genome.wustl.edu
Wellcome Trust Sanger Institute
www.sanger.ac.uk
Whitehead Institute/MIT Center for Genome Research
www.-genome.wi.mit.edu
Ensembl genome annotator European Bionformatics Institute NCBI -
www.ensembl.org
www.ebi.ac.uk
www.ncbi.nlm.nih.gov
Nature Genome Gateway
http://www.nature.com/genomics/human/
Integrated Genomics
http://wit.integratedgenomics.com/GOLD/
Ebi genome databases
http://www2.ebi.ac.uk/genomes/
Primate Sequencing Projects
http://sayer.lab.nig.jp/~silver/index.html
European Bioinformatics Institute Proteomics
http://www.ebi.ac.uk/proteome/
National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/
HapMap Project Homepage
http://www.hapmap.org/
Online Inheritance in Man
http://www.ncbi.nlm.nih.gov/omim/