Hoofdstuk 21 2008

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Hoofdstuk 21 2008

  1. 1. Chapter 21 Genomes and their evolution <ul><li>Contents of chapter 21 </li></ul><ul><li>DNA technology, genomics </li></ul><ul><li>Bioinformatics </li></ul><ul><li>Genomes </li></ul><ul><li>Genome properties </li></ul><ul><li>Genome changes </li></ul><ul><li>Evolutionary genomes </li></ul>
  2. 2. 2 How to sequence a whole genome? <ul><li>Genomics </li></ul><ul><ul><li>Genome: all hereditary information) </li></ul></ul><ul><ul><li>Study of genes, their relationships, their interactions </li></ul></ul><ul><ul><li>Sequence genomes </li></ul></ul><ul><ul><li>Analysis tool: bioinformatics </li></ul></ul><ul><li>Bioinformatics </li></ul><ul><li>Genome properties </li></ul><ul><li>Genome changes </li></ul><ul><li>Evolutionary genomes </li></ul>Three steps towards sequencing a genome
  3. 3. 3 Another approach: whole-genome shotgun sequencing <ul><li>Used by public consortium </li></ul><ul><li>Step 4 proved difficult </li></ul>
  4. 4. 3 Another approach: whole-genome shotgun sequencing <ul><li>Used by public consortium </li></ul><ul><li>Step 4 proved difficult </li></ul>
  5. 5. 3 Another approach: whole-genome shotgun sequencing <ul><li>Used by public consortium </li></ul><ul><li>Step 4 proved difficult </li></ul>
  6. 6. 3 Another approach: whole-genome shotgun sequencing <ul><li>Used by public consortium </li></ul><ul><li>Step 4 proved difficult </li></ul>
  7. 7. Table 1 Genome sizes and estimated number of genes How to analyze all the sequence information?
  8. 8. 4 Bioinformatics DNA analysis <ul><li>Relatively new science field </li></ul><ul><li>Computer </li></ul><ul><li>www </li></ul>
  9. 9. 4 Bioinformatics DNA analysis <ul><li>Relatively new science field </li></ul><ul><li>Computer </li></ul><ul><li>www </li></ul>
  10. 10. 5 Bioinformatics protein analysis <ul><li>Proteomics </li></ul><ul><ul><li>Study of all proteins </li></ul></ul><ul><ul><ul><li>Proteins do the job! </li></ul></ul></ul><ul><ul><ul><li>Analysis of interactions between proteins </li></ul></ul></ul><ul><li>Transcriptome? </li></ul><ul><li>Metabolomics? </li></ul>
  11. 11. 5 Bioinformatics protein analysis <ul><li>Proteomics </li></ul><ul><ul><li>Study of all proteins </li></ul></ul><ul><ul><ul><li>Proteins do the job! </li></ul></ul></ul><ul><ul><ul><li>Analysis of interactions between proteins </li></ul></ul></ul>
  12. 12. 5 Bioinformatics protein analysis <ul><li>Proteomics </li></ul><ul><ul><li>Study of all proteins </li></ul></ul><ul><ul><ul><li>Proteins do the job! </li></ul></ul></ul><ul><ul><ul><li>Analysis of interactions between proteins </li></ul></ul></ul><ul><li>Transcriptome? </li></ul><ul><li>Metabolomics? </li></ul>
  13. 13. 7 Human noncoding DNA <ul><li>Transposable elements </li></ul><ul><ul><li>Remnants from viruses? </li></ul></ul><ul><li>Repetitive DNA </li></ul><ul><ul><li>Short tandem repeat (Ch 20!) </li></ul></ul><ul><ul><ul><li>100,000 copies per site of for ex. GTTAC </li></ul></ul></ul><ul><li>Only few % is coding </li></ul><ul><ul><li>Exon? </li></ul></ul><ul><ul><li>rRNA! </li></ul></ul><ul><li>25% is coding </li></ul><ul><ul><li>Including regulatory sequences and introns </li></ul></ul>
  14. 14. 8 Mobile genetic elements <ul><li>Mutations by mobile genetic elements </li></ul><ul><ul><li>Transposons </li></ul></ul>Barbara McClintock
  15. 15. 8 Mobile genetic elements <ul><li>Mutations by mobile genetic elements </li></ul><ul><ul><li>Transposons </li></ul></ul>Barbara McClintock
  16. 16. 8 Mobile genetic elements <ul><li>Mutations by mobile genetic elements </li></ul><ul><ul><li>Transposons </li></ul></ul>Barbara McClintock or cut
  17. 17. 8 Mobile genetic elements <ul><li>Mutations by mobile genetic elements </li></ul><ul><ul><li>Transposons </li></ul></ul>Barbara McClintock or cut
  18. 18. 10 Coding DNA, but repetitive <ul><li>Multigene families </li></ul><ul><ul><li>Globins, Hox </li></ul></ul><ul><ul><li>Often clustered in genome </li></ul></ul><ul><li>Multicopy familie </li></ul><ul><ul><li>rRNA </li></ul></ul><ul><ul><ul><li>Several clusters, each 10 5 copies </li></ul></ul></ul>
  19. 19. 11 Duplication, rearrangement of DNA
  20. 20. 11 Duplication, rearrangement of DNA <ul><li>Blocks of genes in mouse and human together </li></ul><ul><ul><li>Common ancestor? </li></ul></ul>
  21. 21. 12 Duplication during meiosis <ul><li>Recombination between non-sister chromatids </li></ul>
  22. 22. 13 Model for the evolution of globin genes <ul><li>Took a few years…… </li></ul><ul><li>Green are pseudogenes </li></ul>
  23. 23. T21.2 Similarity between human globin genes More similarity, closer relationship?
  24. 24. 14 Exon shuffling Creation and evolution of a new gene <ul><li>Often, exons contain a specific function </li></ul><ul><ul><li>Encode a protein domain with a function </li></ul></ul>
  25. 25. Transposable elements and evolution <ul><li>Promote recombination </li></ul><ul><ul><li>Provide homologous regions </li></ul></ul><ul><ul><ul><li>Required for recombination </li></ul></ul></ul><ul><li>Disrupt genes </li></ul><ul><ul><li>Coding </li></ul></ul><ul><ul><li>Regulatory sequences </li></ul></ul><ul><ul><li>Carry genes or exons to new location </li></ul></ul><ul><li>Create exons </li></ul><ul><ul><li>Alu repeat element can land in intron, creating a splice site </li></ul></ul><ul><li>All changes can be detrimental, neutral, or beneficiary! </li></ul>
  26. 26. 15 Evolution and genomes Comparing genomes gives clues about evolution
  27. 27. 16 Development and genomes Comparing genomes gives clues about development <ul><li>Homologous </li></ul><ul><ul><li>genes </li></ul></ul><ul><ul><li>proteins </li></ul></ul><ul><ul><li>functions </li></ul></ul><ul><ul><li>organisms… </li></ul></ul>Hox genes Evo-devo
  28. 28. 16 Development and genomes Comparing genomes gives clues about development <ul><li>Homologous </li></ul><ul><ul><li>genes </li></ul></ul><ul><ul><li>proteins </li></ul></ul><ul><ul><li>functions </li></ul></ul><ul><ul><li>organisms… </li></ul></ul>Hox genes Evo-devo
  29. 29. 18 Differences in Hox-gene expression <ul><li>Why is every thorax segment the same in the shrimp? </li></ul><ul><li>How changes in Hox-gene expression change how you look like </li></ul>
  30. 30. Summary of Chapter 21 <ul><li>Sequencing genomes </li></ul><ul><li>Analysis </li></ul><ul><ul><li>Coding and non-coding </li></ul></ul><ul><ul><ul><li>Junk?? </li></ul></ul></ul><ul><li>Comparisons </li></ul><ul><li>Conclusions about </li></ul><ul><ul><li>Evolution </li></ul></ul><ul><ul><li>Development </li></ul></ul><ul><li>Of genes, proteins, processes, organisms… </li></ul>Changes in FoxP2 protein between: chimpanzee orangutan gorilla macaque mouse human . Which amino acids are important for speech?

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