Center for Biological Sequence Analysis The Technical University of Denmark DTU Chromatin and Gene Expression in E. coli Dave Ussery Biological Sequence.

Slides:

Advertisements

Similar presentations

Introduction to perl programming: the minimum to know! Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China.

Advertisements

Supplementary Figure S1 (A) Change of reporter activity levels after actinomycin D treatment. HEK293T cells were transiently transfected with the reporter.

Uses of Cloned Genes sequencing reagents (eg, probes) protein production insufficient natural quantities modify/mutagenesis library screening Expression.

Huntington Disease An overview

The genetic code.

Center for Biological Sequence Analysis Prokaryotic gene finding Marie Skovgaard Ph.D. student

Protein Synthesis (making proteins)

 -GLOBIN MUTATIONS AND SICKLE CELL DISORDER (SCD) - RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLP)

ATG GAG GAA GAA GAT GAA GAG ATC TTA TCG TCT TCC GAT TGC GAC GAT TCC AGC GAT AGT TAC AAG GAT GAT TCT CAA GAT TCT GAA GGA GAA AAC GAT AAC CCT GAG TGC GAA.

Supplementary Fig.1: oligonucleotide primer sequences.

Gene Mutations Worksheet

Transcription & Translation Worksheet

title Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Genomics of five Clostridium species Comparative Microbial.

Crick’s early Hypothesis Revisited. Or The Existence of a Universal Coding Frame Axel Bernal UPenn Center for Bioinformatics Jean-Louis Lassez Coastal.

1 Essential Computing for Bioinformatics Bienvenido Vélez UPR Mayaguez Lecture 5 High-level Programming with Python Part II: Container Objects Reference:

 Genetic information, stored in the chromosomes and transmitted to the daughter cells through DNA replication is expressed through transcription to RNA.

In vitro expression of BVDV capsid protein Corpus Christi College, University of Oxford Glycobiology Institute, Department of Biochemistry KOR SHU CHAN.

Today… Genome 351, 8 April 2013, Lecture 3 The information in DNA is converted to protein through an RNA intermediate (transcription) The information in.

GENE MUTATIONS aka point mutations. DNA sequence ↓ mRNA sequence ↓ Polypeptide Gene mutations which affect only one gene Transcription Translation © 2010.

Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics group Towards a “Systems Microbiology” of.

IGEM Arsenic Bioremediation Possibly finished biobrick for ArsR by adding a RBS and terminator. Will send for sequencing today or Monday.

 The following material is the result of a curriculum development effort to provide a set of courses to support bioinformatics efforts involving students.

Nature and Action of the Gene

Biological Dynamics Group Central Dogma: DNA->RNA->Protein.

Math 15 Introduction to Scientific Data Analysis Lecture 10 Python Programming – Part 4 University of California, Merced Today – We have A Quiz!

Undifferentiated Differentiated (4 d) Supplemental Figure S1.

A.B. C. orf60(pOrf60) 042orf orf60(pOrf60-M5 ) orf60(pOrf60-M1) orf60(pOrf60-M4) 042orf60 042orf60(pOrf60-M5) orf60(pOrf60) 042orf60(pOrf60-M1)

Supplemental Table S1 For Site Directed Mutagenesis and cloning of constructs P9GF:5’ GAC GCT ACT TCA CTA TAG ATA GGA AGT TCA TTT C 3’ P9GR:5’ GAA ATG.

Lecture 10, CS5671 Neural Network Applications Problems Input transformation Network Architectures Assessing Performance.

Fig. S1 siControl E2 G1: 45.7% S: 26.9% G2-M: 27.4% siER  E2 G1: 70.9% S: 9.9% G2-M: 19.2% G1: 57.1% S: 12.0% G2-M: 30.9% siRNF31 E2 A B siRNF31 siControl.

PART 1 - DNA REPLICATION PART 2 - TRANSCRIPTION AND TRANSLATION.

TRANSLATION: information transfer from RNA to protein the nucleotide sequence of the mRNA strand is translated into an amino acid sequence. This is accomplished.

Today… Genome 351, 8 April 2013, Lecture 3 The information in DNA is converted to protein through an RNA intermediate (transcription) The information in.

 The following material is the result of a curriculum development effort to provide a set of courses to support bioinformatics efforts involving students.

NSCI 314 LIFE IN THE COSMOS 4 - The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB

Prodigiosin Production in E. Coli Brian Hovey and Stephanie Vondrak.

Passing Genetic Notes in Class CC106 / Discussion D by John R. Finnerty.

Supplementary materials

Dictionaries. A “Good morning” dictionary English: Good morning Spanish: Buenas días Swedish: God morgon German: Guten morgen Venda: Ndi matscheloni Afrikaans:

Suppl. Figure 1 APP23 + X Terc +/- Terc +/-, APP23 + X Terc +/- G1Terc -/-, APP23 + X G1Terc -/- G2Terc -/-, APP23 + X G2Terc -/- G3Terc -/-, APP23 + and.

Structure and Function of DNA DNA Replication and Protein Synthesis.

RA(4kb)- Atggagtccgaaatgctgcaatcgcctcttctgggcctgggggaggaagatgaggc……………………………………………….. ……………………………………………. ……………………….,……. …tactacatctccgtgtactcggtggagaagcgtgtcagatag.

Example 1 DNA Triplet mRNA Codon tRNA anticodon A U A T A U G C G

Topic: Replication of DNA Standard: Explain the role of DNA in storing and transmitting cellular information.

DNA, RNA and Protein.

The response of amino acid frequencies to directional mutation pressure in mitochondrial genomes is related to the physical properties of the amino acids.

Figure S1. Construction of pAL70

Fundamentals of Protein Structure

Modelling Proteomes.

Supplementary information Table-S1 (Xiao)

Sequence – 5’ to 3’ Tm ˚C Genome Position HV68 TMER7 Δ mt. Forward

Supplemental Table 3. Oligonucleotides for qPCR

Laboratory Encounters in Plant Genomics

GENE MUTATIONS aka point mutations © 2016 Paul Billiet ODWS.

Supplementary Figure 1 – cDNA analysis reveals that three splice site alterations generate multiple RNA isoforms. (A) c.430-1G>C (IVS 6) results in 3.

Huntington Disease (HD)

DNA By: Mr. Kauffman.

Gene architecture and sequence annotation

Schematic of the PCR assay.

PROTEIN SYNTHESIS RELAY

Molecular engineering of photoresponsive three-dimensional DNA

Fundamentals of Protein Structure

Laboratory Encounters in Plant Genomics

Station 2 Protein Synethsis.

6.096 Algorithms for Computational Biology Lecture 2 BLAST & Database Search Manolis Piotr Indyk.

Shailaja Gantla, Conny T. M. Bakker, Bishram Deocharan, Narsing R

Presentation transcript:

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 # April, 2005

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

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

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

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

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

Center for Biological Sequence Analysis The Technical University of Denmark DTU

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

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

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

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

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

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

Center for Biological Sequence Analysis The Technical University of Denmark DTU

TATA

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

Center for Biological Sequence Analysis The Technical University of Denmark DTU

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

Center for Biological Sequence Analysis The Technical University of Denmark DTU

nucleosomes

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

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

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

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

Center for Biological Sequence Analysis The Technical University of Denmark DTU travers trinuc. % Out AAT/ATT AAA/TTT CCA/TGG AAC/GTT ACT/AGT CCG/CGG ATC/GAT AAG/CTT CGC/GCG AGG/CCT GAA/TTC ACG/CGT ACC/GGT GAC/GTC CCC/GGG ACA/TGT CGA/TCG GGA/TCC CAA/TTG AGC/GCT GTA/TAC AGA/TCT CTC/GAG CAC/GTG TAA/TTA GCA/TGC CTA/TAG GCC/GGC ATG/CAT CAG/CTG ATA/TAT TCA/TGA “Travers” trinucleotide scale: Satchwell,S.C., Drew,H.R., and Travers,A.A., "Sequence periodicities in chicken nucleosome core DNA",J. Mol. Biol.,191 : , (1986) Baldi,P., Brunak,S., Chauvin,Y., and Krogh,A., "Naturally occurring nucleosome positioning signals in human exons and introns",J. Mol. Biol.,263 : , (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.

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

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).

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

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

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

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

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

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

Biochimie, 83: , (2001).

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

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

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

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

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).

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: (2001).

Center for Biological Sequence Analysis The Technical University of Denmark DTU

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!