Evolution of gene expression and gene-regulatory sequences in Drosophila melanogaster [Elektronische Ressource] / Sarah Sylvie Saminadin-Peter

Sarah Saminadin-Peter

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2008
• Nombre de lectures: 79
• Langue: Deutsch
• Poids de l'ouvrage: 2 Mo

Extrait

Dissertation zur Erlangung des Doktorgrades
der Naturwissenschaften an der Fakultät für Biologie
der Ludwig-Maximilians-Universität München













Evolution of gene expression and
gene-regulatory sequences
in Drosophila melanogaster











Sarah Sylvie Saminadin-Peter
aus
Basse-Terre, Guadeloupe
2008 Erklärung

Diese Dissertation wurde im Sinne von §12 der Promotionsordnung von Prof. Dr.
John Parsch betreut. Ich erkläre hiermit, dass die Dissertation nicht einer anderen
Prüfungskommission vorgelegt worden ist und dass ich mich nicht anderweitig einer
Doktorprüfung ohne Erfolg unterzogen habe.




Ehrenwörtliche Versicherung

Ich versichere hiermit ehrenwörtlich, dass die vorgelegte Dissetation von mir
selbständig, ohne unerlaubte Hilfe angefertigt wurde.





München, 04.11.2008




Sarah Saminadin-Peter
















1.Gutachter: Prof. Dr. John Parsch
2.Gutachter: Prof. Wolfgang Stephan





Dissertation eingereicht am: 04.11.2008
Mündliche Prüfung am: 05.12.2008 Table of contents
Table of contents

Note ............................................................................................................................................ 5
List of Abbreviations.................................................................................................................. 6
Zusammenfassung...................................................................................................................... 8
General Introduction ................................................................................................................ 10

Chapter 1 Gene expression variation in African and European populations of
Drosophila melanogaster ........................................................................................................ 17
1.1 Introduction.............................................................................................................. 17
1.2 Materials and Methods............................................................................................. 19
1.3 Results...................................................................................................................... 23
1.4 Discussion................................................................................................................ 36

Chapter 2 Validation of microarray results and comparison of patterns of expression
variation in males and females of Drosophila melanogaster............................................... 41
2.1 Introduction 41
2.2 Material and Methods............................................................................................... 44
2.3 Results and Discussion............................................................................................. 46

Chapter 3 The relationship between gene expression polymorphism and DNA sequence
polymorphism in coding and non-coding regions of genes in natural populations of
Drosophila melanogaster ........................................................................................................ 54
3.1 Introduction.............................................................................................................. 54
3.2 Materials and Methods 56
3.3 Results and Discussion 58

Chapter 4 Evidence for a selective sweep in the regulatory region of a gene that differs
in expression between European and African populations of Drosophila melanogaster . 85
4.1 Introduction 85
4.2 Materials and Methods............................................................................................. 88
4.3 Results...................................................................................................................... 92
4.4 Discussion.............................................................................................................. 104

Summary ................................................................................................................................ 107
Literature cited ....................................................................................................................... 109
1 Table of contents

Appendix A ............................................................................................................................ 122
Appendix B ........ 129
Appendix C ........ 132
Appendix D ........ 136
Appendix E ............................................................................................................................ 139
Appendix F 151
Curriculum Vitae.................................................................................................................... 152
Publications and Presentations............................................................................................... 153
Acknowledgements. 154


2 List of tables and figures
List of tables and figures


Table 1: Statistical power of the experiments to detect expression differences....................... 23
Table 2: Number of significant tests and false discovery rates................................................ 24
Table 3: Polymorphism in expression...................................................................................... 25
Table 4: Expression polymorphism on the X chromosome and autosomes ............................ 29
Table 5: Expression variation in sex-biased genes................................................................... 30
Table 6: GO terms over-represented ........................................................................................ 34
Table 7: Comparison of quantitative PCR and microarray measurements of adult male and
female gene expression differences between populations..................................................... 47
Table 8: Sex-biased expression of genes according to the Sebida database ............................ 48
Table 9: List of the genes used for this study........................................................................... 59
Table 10: Polymorphism and divergence in coding and non-coding regions. ......................... 60
Table 11: Genes with significant McDonald-Kreitman tests ................................................... 64
Table 12: Frequency of derived mutations in the African and European populations............. 79
Table 13: Relative levels of gene expression for four genes in the cenG1A region. ............... 82
Table 14: Relative levels of gene expression for CG7916 and CG8997 in the European and
African populations............................................................................................................... 82
Table 15: Gene expression data for the CG9509 gene............................................................. 92
Table 16: McDonald-Kreitman test for the CG9509 and CG14406 genes.............................. 95
Table 17: Tajima’s D values for synonymous, non-synonymous, intergenic and intron sites:96
Table 18: Maximum-Likelihood analysis ................................................................................ 98
Table 19: Fixed (or nearly fixed) differences between European and African ..................... 102

Figure 1: Principle of cDNA microarray assay........................................................................ 11
Figure 2: The interactions between transcription factor proteins ............................................ 13
Figure 3: Distribution of new variants in haplotypes in three different classes of sequences . 14
Figure 4: Microarray experimental design............................................................................... 20
Figure 5: Complete pairwise comparison matrix. .................................................................... 27
Figure 6: Neighbor-joining trees of the 16 D. melanogaster. .................................................. 28
Figure 7: Volcano plot of gene expression differences between European and African
populations.. .......................................................................................................................... 31
Figure 8: Chromosomal location of significant differentially expressed genes between Europe
and Africa.............................................................................................................................. 32
3 List of tables and figures
Figure 9: Specific tissue enrichment for genes significantly differentially expressed between
Europe and Africa ................................................................................................................. 33
Figure 10: Top-ten list of the genes over-expressed in each population with P < 0.002......... 35
Figure 11: Quantitative Real-Time PCR using the on TaqMan method.................................. 42
Figure 12: Principle of qPCR analysis for a single sample model........................................... 45
Figure 13: Correlation betw