Identification of large-scale DNA copy number differences between human and non-human primate genomes and their role in mediating evolutionary rearrangements [Elektronische Ressource] / presented by Violaine Goidts

Violaine Goidts

Sujets

• Gesundheit

Informations

• Publié par: universitat_ulm
• Publié le: 01 janvier 2006
• Nombre de lectures: 17
• Langue: English
• Poids de l'ouvrage: 2 Mo

Extrait

University of Ulm
Department of Human Genetics
Prof. Dr. Walther Vogel




Identification of Large-Scale DNA Copy Number
Differences Between Human and Non-Human Primate
Genomes and their Role in Mediating Evolutionary
Rearrangements



Dissertation
To obtain the doctoral degree of Human Biology
At the Faculty of Medicine, University of Ulm

Presented by
Violaine GOIDTS
from Namur, Belgium


Ulm, 2006


Amtierender Dekan: Prof. Dr. Klaus-Michael Debatin

1. Berichterstatter Prof. Dr. Horst Hameister

2. Berichterstatter Prof. Dr. Werner Schempp

Tag der Promotion: 05.05.2006
Erklärung


Ich versichere hiermit, dass ich die vorliegende Arbeit selbstständig
angefertigt und keine anderen als die angegebenen Quellen und
Hilfsmittel benutzt sowie wörtlich oder inhaltlich übernommene
Textpassagen als solche gekennzeichnet habe.




Ulm, 27.01.2006




Violaine GOIDTS


























“Most scientific theories either deal with questions
that only interest specialists or require a forbidding set
of technical skills before you can understand them.
The theory of evolution is scientifically unique in its
combination of universal interests and accessibility.”


ndMark Ridley, Evolution 2 Edition.
Table of content

1. INTRODUCTION _______________________________________________ 10
1.1. Importance to do the human-chimpanzee comparison _________________ 10
1.2. Differences between human and non-human primate genomes __________ 12
1.2.1. Nucleotide divergence ______________________________________________ 12
1.2.2. Karyotypic differences______________________________________________ 13
1.2.3. Sub-microscopic differences ________________________________________ 14
1.2.4. Copy number differences: a class of micro-differences in itself____________ 16
1.3. The array comparative genomic hybridization (aCGH) technique_________ 24
1.4. Objective of the study ____________________________________________ 26
2. MATERIALS AND METHODS _____________________________________ 27
2.1. Materials _______________________________________________________ 27
2.1.1. Oligonucleotides __________________________________________________ 27
2.1.2. DNA samples _____________________________________________________ 29
2.1.3. Cell lines _________________________________________________________ 30
2.1.4. BAC clones _______________________________________________________ 31
2.1.5. Chemicals and reagents ____________________________________________ 32
2.1.6. Enzymes _________________________________________________________ 34
2.1.7. Antibodies________________________________________________________ 34
2.1.8. Equipment________________________________________________________ 34
2.1.9. Kits______________________________________________________________ 35
2.2. Methods________________________________________________________ 36
2.2.1. DNA technology ___________________________________________________ 36
2.2.2. RNA technology ___________________________________________________ 46
2.2.3. Cell technology____________________________________________________ 47
2.2.4. Chromosome technology ___________________________________________ 48
2.2.5. In silico analysis___________________________________________________ 52
3. RESULTS _____________________________________________________ 54
3.1. Study of micro-differences between human and primate genomes._______ 54
3.1.1. Number of differences detected by aCGH in primate genomes_____________ 54
3.1.2. High number of species-specific rearrangements in the gorilla lineage _____ 59
3.1.3. Human-specific rearrangements______________________________________ 61
3.1.4. Ancestral loci of the HLS-CND-detecting DCs___________________________ 71
3.1.5. Boundaries of putative HLS-CNDs and their respective homologous DCs ___ 72
3.2. Study of two macro-differences between human and primate genomes:
examples of evolutionary rearrangements driven by LCRs____________________ 74
3.2.1. The pericentric inversion of chimpanzee and gorilla chromosomes homologous
to human chromosome 16 ___________________________________________________ 74
3.2.2. The human specific pericentric inversion of chromosome 18______________ 86
4. DISCUSSION __________________________________________________ 92
4.1. Characterization of DNA copy number differences between human and non-
human primates _______________________________________________________ 92
4.2. Human-specific copy number differences ____________________________ 94
4.3. Genes contained in the putative HLS-CNDs __________________________ 96
4.4. Polymorphisms vs. differences fixed in the human population __________ 97
4.5. Presence of evolutionary young repeat sequences at the boundaries of the
DCs identified _________________________________________________________ 99
4.6. Non-random distribution of CNDs _________________________________ 100
4.6.1. CNDs localized in regions of chromosomal instability___________________ 100
4.6.2. CNDs localized in the vicinity of evolutionary chromosomal breakpoints ___ 101
4.6.3. Pericentric inversions of chromosomes 16 and 18, further examples of
rearrangements driven by LCRs _____________________________________________ 102
4.7. Final conclusion ________________________________________________ 108
5. REFERENCES ________________________________________________ 109
6. SUMMARY ___________________________________________________ 131
7. APPENDIX ___________________________________________________ 132
Abbreviations

aCGH Array Comparative Genomic Hybridization
AIDS Acquired Immunodeficiency Syndrome
ANAPC1 Anaphase Promoting Complex Subunit 1
BAC Bacterial Artificial Chromosome
BLAST Basic Local Alignment Search Tool
Bp Base Pair
cDNA Complementary DNA
CND Copy Number Difference
CTD California Institute of Technology library D
DC Duplication Cluster
DNA Desoxyribonucleic Acid
dNTP Deoxynucleoside Triphosphate
EBV Epstein Barr Virus
ECACC European Collection of Cell Cultures
EST Expressed Sequence Tag
FISH Fluorescence In Situ Hybridization
FMRPD2 FERM and PDZ Domain Containing 2
FOXP2 Forkhead Box P2
GGO Gorilla gorilla
HLS Human Lineage Specific
HPRT Hypoxanthine-Guanine Phosphoribosyltransferase
HSA Homo sapiens
Kb Kilobase
Mb Megabase
MFA Macaca fascicularis
MFU Macaca fuscata
mRNA messenger RNA
Mya Million years ago
Myrs Million years
NHEJ Non Homologous End Joining
PCR Polymerase Chain Reaction
PPA Pan paniscus
PPY Pongo pygmaeus
PTR Pan troglodytes
RNA Ribonucleic Acid
ROCK1 Rho-Associated Coiled-Coil Containing Protein Kinase 1
RP Roswell Park
SHCBP1 Shc SH2-Domain Binding Protein 1
SNP Single Nucleotide Polymorphism
TAR Telomere Associated Repeat
THOC1 THO Complex Subunit 1
USP14 Ubiquitin Specific Protease 14
UTR Untranslated Region
mM Micromolar
mg Microgramm
ml Microliter INTRODUCTION 10
1. INTRODUCTION

1.1. Importance to do the human-chimpanzee
comparison

“What sets us apart from other species?” is what interests the most the humans. One
of the important ways to answer this question is to compare the human genome with
the genomes of other species. Up until the end of year 2003, the limited availability of
complete genome sequences reduced such comparisons to species such as mouse,
fish, and worm, which are distantly related to humans. These comparisons are
relevant to understand what is common to all mammals, all vertebrates, or all
animals, but uninformative with regard to what is unique to primates (Enard and
Pääbo, 2004).
This situation changed radically with the completion of the draft sequence of the
chimpanzee genome (Chimpanzee Sequencing and Analysis Consortium, 2005).
Humans and chimpanzees diverged about 5 - 6 million years ago, making the
chimpanzee the closest relative to human (Goodman et al., 1999; Glazko and Nei,
2003) (Figure 1.1).
Since the chimpanzee genome shows remarkable similarity to that of humans, it will
help us to understand the hominines evolution and to determine the genetic basis of
human uniqueness.
Moreover, human-chimpanzee comparisons also have more practical implications.
Indentifying genes that are divergent between humans and chimpanzees may be
extremely helpful in understanding disease susceptibility. For example, even though
the chimpanzee DNA sequence is 98.77 % identical to that of the human (Chen and
Li, 2001; Ebersberger et al., 2002; Chimpanzee Sequencing and Analysis
Consortium, 2005), chimpanzees do not suffer from some diseases that strike
humans, such as AIDS, Plasmodium falcipar