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Comparative Microbial Genomics Group. Center for Biological Sequence Analysis The Technical University of Denmark DTU. title. Part 2: Gene Expression and Chromatin Structure In Bacterial Genomes. Dave Ussery Advanced Bioinformatics course lecture 14 November, 2003.

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  1. Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU title Part 2: Gene Expression and Chromatin Structure In Bacterial Genomes Dave Ussery Advanced Bioinformatics course lecture 14 November, 2003

  2. Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU Spombe zoom

  3. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E. coli Affy Mol. Genet. Genomics, 267:721-729, (2001).

  4. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group niceDogma

  5. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C. jejuni Genome

  6. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy Cold ShockExpress Data kindly provided by Alain Stintzi, Genome Letters, 2:18-27, (2003).

  7. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy Heat shock J. Bact., 185:2009-2016, (2003). CHRO2003

  8. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy Heat shock

  9. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy exp2

  10. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy exp. 1

  11. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Origin of replication figure

  12. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy Heat shock J. Bact., 185:2009-2016, (2003). CHRO2003

  13. E. coli chromatin

  14. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Chromatin proteins

  15. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E. coli chromatin IHF Biochimie, 83:201-212, (2001).

  16. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E. Coli chromatin FIS Biochimie, 83:201-212, (2001).

  17. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Fis unsmoothed

  18. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Fis smoohted

  19. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Smoothed Chromatin Biochimie, 83:201-212, (2001).

  20. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E. coli hundred exps

  21. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Future of microarrays What is the future of microarrays?

  22. Ecoli Genomic Landscape anaerobic growth, alcohol metabolism, acid response aerobic growth, oxidation Center for Biological Sequence Analysis The Technical University of Denmark DTU protein synthesis Comparative Microbial Genomics Group cell cycle control stress electron transport membrane, secretion DNA replication, flagella biosynthesis Ecoli genomic landscape Genomic landscape of E. coli kindly provided by Josh Stuart, Stanford; Science, 293:2087-2092 (2001). Data kindly provided by Alain Stintzi CHRO2003

  23. Closer look

  24. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E.coli promoters map1 Mol. Genet. Genomics, 267:721-729, (2001).

  25. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group E.coli promoters map2

  26. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Promoter cartoon Promoter cartoon DNA melting important here rigid DNA curvature, flexibility important here -35 -10 b / b’ s a Promoter cartoon

  27. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group More on sigmas J. Mol. Biol., 299:907-930, (2000).

  28. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Number Sigmas/genome

  29. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Sigma70s Blue Proteobacteria ’s RpoE RpoH FliA RpoS RpoD

  30. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Sigma70s with colour Proteobacteria ’s a subdivision b subdivision g subdivision e subdivision RpoE RpoH FliA RpoS RpoD

  31. Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group RpoD vs. RpoS

  32. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group summary Summary 1. Chromatin structure is important in bacteria 2. Where you are in the chromosome is important! 3. The number of sigma factors per genome can vary greatly between different bacteria.

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