C e n t e r f o r B i o l o g i c a l S e q u e n c e A n a l y s i s T h e T e c h n i c a l U n i v e r s i t y o f D e n m a r k D T U Chromatin and Gene Expression in E. coli Dave Ussery Biological Sequence Analysis DTU course # 27803 15 April, 2005
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Center for Biological Sequence Analysis The Technical University of Denmark DTU Chromatin and Gene Expression in E. coli Dave Ussery Biological Sequence.
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Cen
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Chromatin andGene Expression
in E. coli
Dave UsseryBiological Sequence AnalysisDTU course # 2780315 April, 2005
Satchwell,S.C., Drew,H.R., and Travers,A.A., "Sequence periodicities in chicken nucleosome core DNA" ,J. Mol. Biol. ,191 :659-675, (1986)
Baldi,P., Brunak,S., Chauvin,Y., and Krogh,A., "Naturally occurring nucleosome positioning signals in human exons and introns" ,J. Mol. Biol. ,263 :503-510, (1996). )
NOTE: we use a (slight) modification,in which the absolute value (magnitude) of the values is used to reflect trinucleotideswhich tend to exclude nucleosomes.
Low position pref.
Highposition pref.
Highposition pref.
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Spombe - 3 chromosomes
Nature, 415:871-880, (2002).
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S.pombe chr. 1
DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004).
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Spombe zoom
DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004).
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• Chromatin proteins in bacteria • Gene Expression in bacteria
Part the last:
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J. Mol. Biol, 299:907-930, (2000).
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J. Mol. Biol, 299:907-930, (2000).
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Highly Expressed Genes
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niceDogma
Comparative Microbial Genomics Group
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Cen
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Cen
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Biochimie, 83:201-212, (2001).
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Biochimie, 83:201-212, (2001).
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Biochimie, 83:201-212, (2001).
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Biochimie, 83:201-212, (2001).
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Biochimie, 83:201-212, (2001).
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plectonemic supercoils
Curved DNA
RNA polymerase
torroidal supercoiling
topological boundry
Genome Biology, 5:252, (2004).
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Ecoli Genomic Landscape
Ecoli genomic landscape
Comparative Microbial Genomics Group
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CHRO2003Data kindly provided by Alain Stintzi
protein synthesis
electron transport
DNA replication,flagella biosynthesis
anaerobic growth,alcohol metabolism,acid response
stress
membrane, secretion
aerobic growth, oxidation
cell cyclecontrol
Genomic landscape of E. coli kindly provided by Josh Stuart, Stanford; Science, 293:2087-2092 (2001).
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Summary
1. DNA sequence DNA structure Function
2. DNA curvature is caused mainly by phased A-tracts.