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Cen
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Chromatin andGene Expression
in E. coli
Dave UsseryBiological Sequence AnalysisDTU course # 2780315 April, 2005
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Outline
• Introduction & disclaimer
• DNA structures: curvature & Position preference
• Chromatin and Gene Expression
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• Regulation of Gene Expression in Bacteria
Part the first:Introduction
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Mol. Genet. Genomics, 267:721-729, (2001).
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Genome Biology, 5:252, (2004).
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1. What is Regulated?
2. How is it Regulated?
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http://string.embl.de/
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Three levels of Regulation
~100,000 proteins/cell
~1,000 proteins/cell
1. Global - chromatin
2. Sigma factors
3. Transcription factors10 to 100 proteins/cell
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1. Global - chromatin
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2. Sigma factors
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Proteobacteria
Firmicutes
Actinobacteria
σ54
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Sig70 tree
Firmicutes
Actinobacteria
σ70
ChlamydiaCyanobact.
“other phyla”
RpoDRpoS
sigEsporulationiniation
RpoH
sigFsporulation
sigGsporulation
RpoFflagella
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• DNA curvature • Position preference
Part the second:
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Cen
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Cen
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Cen
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Cen
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Cen
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-35
-10 TATA
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J. Mol. Biol., 299:907-930, (2000).
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Cen
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Cen
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Promoter Structural profile
+1
CDS
DNA curvature,flexibility importanthere
meltsrigid
cruciform
-10-35
mRNACDS
ββ’
-10-35
+1
σα
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Cen
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nucleosomes
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chromatin
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Beads on a string
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Trimmed 1
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Trimmed 2
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travers
trinuc. % Out AAT/ATT -0.280 AAA/TTT -0.274 CCA/TGG -0.246 AAC/GTT -0.205 ACT/AGT -0.183 CCG/CGG -0.136 ATC/GAT -0.110 AAG/CTT -0.081 CGC/GCG -0.077 AGG/CCT -0.057 GAA/TTC -0.037 ACG/CGT -0.033 ACC/GGT -0.032 GAC/GTC -0.013 CCC/GGG -0.012 ACA/TGT -0.006 CGA/TCG -0.003 GGA/TCC 0.013 CAA/TTG 0.015 AGC/GCT 0.017 GTA/TAC 0.025 AGA/TCT 0.027 CTC/GAG 0.031 CAC/GTG 0.040 TAA/TTA 0.068 GCA/TGC 0.076 CTA/TAG 0.090 GCC/GGC 0.107 ATG/CAT 0.134 CAG/CTG 0.175 ATA/TAT 0.182 TCA/TGA 0.194
“Travers” trinucleotide scale:
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.
3. Where you are in the chromosome is important!
