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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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Presentation on theme: "Center for Biological Sequence Analysis The Technical University of Denmark DTU Chromatin and Gene Expression in E. coli Dave Ussery Biological Sequence."— Presentation transcript:

1 Center for Biological Sequence Analysis The Technical University of Denmark DTU Chromatin and Gene Expression in E. coli Dave Ussery Biological Sequence Analysis DTU course # 27803 15 April, 2005

2 Center for Biological Sequence Analysis The Technical University of Denmark DTU Outline Introduction & disclaimer DNA structures: curvature & Position preference Chromatin and Gene Expression

3 Center for Biological Sequence Analysis The Technical University of Denmark DTU Regulation of Gene Expression in Bacteria Part the first: Introduction

4 Center for Biological Sequence Analysis The Technical University of Denmark DTU Mol. Genet. Genomics, 267:721-729, (2001).

5 Center for Biological Sequence Analysis The Technical University of Denmark DTU Genome Biology, 5:252, (2004).

6 Center for Biological Sequence Analysis The Technical University of Denmark DTU 1. What is Regulated? 2. How is it Regulated?

7 Center for Biological Sequence Analysis The Technical University of Denmark DTU http://string.embl.de/

8 Center for Biological Sequence Analysis The Technical University of Denmark DTU Three levels of Regulation ~100,000 proteins/cell ~1,000 proteins/cell 1. Global - chromatin 2. Sigma factors 3. Transcription factors 10 to 100 proteins/cell

9 Center for Biological Sequence Analysis The Technical University of Denmark DTU 1. Global - chromatin

10 Center for Biological Sequence Analysis The Technical University of Denmark DTU 2. Sigma factors

11 Center for Biological Sequence Analysis The Technical University of Denmark DTU Proteobacteria Firmicutes Actinobacteria  54

12 Center for Biological Sequence Analysis The Technical University of Denmark DTU Sig70 tree Firmicutes Actinobacteria  70 Chlamydia Cyanobact. “other phyla” RpoD RpoS sigE sporulation iniation RpoH sigF sporulation sigG sporulation RpoF flagella

13 Center for Biological Sequence Analysis The Technical University of Denmark DTU DNA curvature Position preference Part the second:

14 Center for Biological Sequence Analysis The Technical University of Denmark DTU

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19 -35 -10 TATA

20 Center for Biological Sequence Analysis The Technical University of Denmark DTU J. Mol. Biol., 299:907-930, (2000).

21 Center for Biological Sequence Analysis The Technical University of Denmark DTU

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23 Promoter Structural profile +1 CDS DNA curvature, flexibility important here melts rigid cruciform -10 -35 mRNA CDS  ’ -10 -35 +1  

24 Center for Biological Sequence Analysis The Technical University of Denmark DTU

25 nucleosomes

26 Center for Biological Sequence Analysis The Technical University of Denmark DTU chromatin

27 Center for Biological Sequence Analysis The Technical University of Denmark DTU Beads on a string

28 Center for Biological Sequence Analysis The Technical University of Denmark DTU Trimmed 1

29 Center for Biological Sequence Analysis The Technical University of Denmark DTU Trimmed 2

30 Center for Biological Sequence Analysis The Technical University of Denmark DTU 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 trinucleotides which tend to exclude nucleosomes. Low position pref. High position pref. High position pref.

31 Center for Biological Sequence Analysis The Technical University of Denmark DTU Spombe - 3 chromosomes Nature, 415:871-880, (2002).

32 Center for Biological Sequence Analysis The Technical University of Denmark DTU S.pombe chr. 1 DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004).

33 Center for Biological Sequence Analysis The Technical University of Denmark DTU Spombe zoom DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004).

34 Center for Biological Sequence Analysis The Technical University of Denmark DTU Chromatin proteins in bacteria Gene Expression in bacteria Part the last:

35 Center for Biological Sequence Analysis The Technical University of Denmark DTU J. Mol. Biol, 299:907-930, (2000).

36 Center for Biological Sequence Analysis The Technical University of Denmark DTU J. Mol. Biol, 299:907-930, (2000).

37 Center for Biological Sequence Analysis The Technical University of Denmark DTU Highly Expressed Genes

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

39

40 Biochimie, 83:201-212, (2001).

41 Center for Biological Sequence Analysis The Technical University of Denmark DTU Biochimie, 83:201-212, (2001).

42 Center for Biological Sequence Analysis The Technical University of Denmark DTU Biochimie, 83:201-212, (2001).

43 Center for Biological Sequence Analysis The Technical University of Denmark DTU Biochimie, 83:201-212, (2001).

44 Center for Biological Sequence Analysis The Technical University of Denmark DTU Biochimie, 83:201-212, (2001).

45 Center for Biological Sequence Analysis The Technical University of Denmark DTU plectonemic supercoils Curved DNA RNA polymerase torroidal supercoiling topological boundry Genome Biology, 5:252, (2004).

46 Center for Biological Sequence Analysis The Technical University of Denmark DTU Ecoli Genomic Landscape Ecoli genomic landscape Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU CHRO2003 Data 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 cycle control Genomic landscape of E. coli kindly provided by Josh Stuart, Stanford; Science, 293:2087-2092 (2001).

47 Center for Biological Sequence Analysis The Technical University of Denmark DTU

48 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!

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