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Gene Expression M.Tevfik DORAK

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1 Gene Expression M.Tevfik DORAK



4 DNA double helix (2-nm diameter) Metaphase chromosome 700 nm Tight helical fiber (30-nm diameter) Nucleosome (10-nm diameter) Histones Beads on a string Supercoil (200-nm diameter) Campbell NE et al (Eds): Biology: Concepts & Connections 4 th Edition, 2003


6 From: Gene Quantification Page by MW Pfaffl

7 Idea: measure the amount of mRNA to see which genes are being expressed in (used by) the cell. Measuring protein might be better, but is currently harder. Gene expression does not always result in a protein product !

8 Transcribed and Nontranscribed Strands

9 From: Vlad Bajic at BioDiscovery Group, Singapore



12 Medical Biochemistry Pages


14 Expression of the human -globin gene. Exons 1 and 3 each contain noncoding sequences (shaded bars) at their extremities, which are transcribed and are present at the 5 and 3 ends of the -globin mRNA, but are not translated to specify polypeptide synthesis. Such 5 and 3 untranslated regions (5 UTR and 3 UTR), however, are thought to be important in ensuring high efficiency of translation. The stop codon UAA represents the first three nucleotides of the 3 untranslated region. Note that the initial translation product has 147 amino acids, but that the N- terminal methionine is removed by post-translational processing to generate the mature b-globin polypeptide. From: Human Molecular Genetics by Strachan & Read. NCBI Books Online

15 From: Principles of Molecular Medicine. LL Jameson (Ed). Humana Press, 1998

16 University of Arizona Biology Project

17 A variety of regulatory proteins interact with DNA and each other Complex assemblies of proteins control eukaryotic transcription Enhancers DNA Activator proteins Other proteins Transcription factors RNA polymerase Bending of DNA Transcription Promoter Gene Campbell NE et al (Eds): Biology: Concepts & Connections 4 th Edition, 2003

18 Chromosome GENE RNA transcript mRNA in nucleus mRNA in cytoplasm Polypeptide ACTIVE PROTEIN GENE Exon Intron Tail Cap NUCLEUS Flow through nuclear envelope CYTOPLASM Breakdown of mRNA TranslationBroken- down mRNA Broken- down protein Cleavage/modification/ activation Breakdown of protein DNA unpacking Other changes to DNA TRANSCRIPTION Addition of cap and tail Splicing Campbell NE et al (Eds): Biology: Concepts & Connections 4 th Edition, 2003


20 A eukaryotic promoter: This promoter contains three promoter elements upstream of the TATA box that are required for efficient transcription: a CCAAT box and two GC boxes (consensus sequence GGGCGG). From: The Cell by GM Cooper. NCBI Online Books



23 Morey AK et al. JBC 1998 ( Chromosomal Location: 6p21.46p21.4 EDN1 Locus: ID 19061906 EDN1 Genome Annotation (chromosome 6 reference genomic contig) : NT_007592NT_007592 EDN1 Genomic Sequence (including the promoter region): J05005J05005

24 EDN1 (GeneID 1906) GI: 340555340555 repeat_regionrepeat_region 98...383 /rpt_family="Alu" protein_bindprotein_bind 739...745 /bound_moiety="acute phase reactant regulatory element" misc_featuremisc_feature 979..1039 /note="Z-DNA region; putative" protein_bindprotein_bind 2183..2188 /bound_moiety="acute phase reactant regulatory element" protein_bindprotein_bind 2951..2958 /bound_moiety="TPA/JUN" protein_bindprotein_bind 3241..3248 /bound_moiety="TPA/JUN" protein_bindprotein_bind 3316..3328 /bound_moiety="NF-1" protein_bindprotein_bind 3499..3505 /bound_moiety="TPA/JUN" CAAT_signalCAAT_signal 3510..3515 /gene="EDN1" TATA_signalTATA_signal 3577..3582 /gene="EDN1" Exon 1Exon 1 3608..3939 /gene="EDN1"

25 Regulatory SNPs

26 Medical Biochemistry Pages

27 Exon 4 12 alternatives Exon 8 48 alternatives Exon 9 33 alternatives Exon 17 2 alternatives DSCAM gene and pre-mRNA Alternative Splicing Can Generate Very Large Numbers of Related Proteins From a Single Gene 12 X 48 X 33 X 2 = alternative mRNAs 38,016 49 of 50 cDNAs sequenced showed alternative splicing suggesting thousands of different proteins from the same gene. mRNA Generating Protein Diversity from the Small Human Genome Black, Cell 103: 367, 2000 splicing

28 Generating Protein Diversity from the Small Human Genome





33 Gene Expression in Prokaryotes Glick and Pasternak Fig. 3.10

34 Three kinds of RNA; Tobin and Duschek, Asking About Life; mRNA: a copy of the gene; is translated to make protein. tRNA: smallest RNA, does actual decoding. rRNA: 3 sizes that, along with proteins, make up a ribosome tRNA rRNA mRNA




38 From: Principles of Molecular Medicine. LL Jameson (Ed). Humana Press, 1998


40 Transcription


42 Maston GA et al. 2006 (www)www

43 Maston GA et al. 2006 (www)www

44 Maston GA et al. 2006 (www)www

45 Maston GA et al. 2006 (www)www

46 Maston GA et al. 2006 (www)www













59 The role of signal sequences in membrane translocation: Signal sequences target the translocation of polypeptide chains across the plasma membrane of bacteria or into the endoplasmic reticulum of eukaryotic cells. The signal sequence, a stretch of hydrophobic amino acids at the amino terminus of the polypeptide chain, inserts into a membrane channel as it emerges from the ribosome. The rest of the polypeptide is then translocated through the channel and the signal sequence is cleaved by the action of signal peptidase, releasing the mature translocated protein. From: The Cell by GM Cooper: NCBI Online Books

60 From: Weissmann & Lyko. BioTechniques 2003 EPIGENETIC CROSSTALK

61 Wellcome Trust


63 Six steps at which eukaryote gene expression can be controlled From: Molecular Biology of the Cell by Alberts B, Bray D, Lewis J, Raff M, Roberts K, and Watson JD. NCBI Books Online



66 Nigel Walker, NIEHS (www) (www)

67 Traditional gene expression analysis: Northern Blotting Northern blotting detects specific RNAs RNA is isolated from cells and separated using electrophoresis probed with radioactive cDNA from a specific gene Method can be used to determine steady-state level of a transcript in a specific RNA mixture

68 Serial analysis of gene expression (SAGE) 9 to 11 base tags correspond to genes measure of gene expression in different biological samples SAGE tags can be compared electronically

69 Serial analysis of gene expression (SAGE) Page 169

70 SAGENet:




74 NUCLEASE PROTECTION ASSAY In this example, an mRNA containing a point mutation (indicated by the inverted triangle in the mRNA on the right) is distinguished from its normal, non-mutated counterpart (mRNA on the left). The mRNA is mixed with a single-stranded 32P- labeled DNA or RNA probe that (1) has sequences perfectly complementary to the nonmutated region of interest in the mRNA, and (2) extends for some length beyond the mRNA. The mixture is heated then cooled to allow the probe to anneal to its complementary sequences in the mRNA. The annealed mixture is then treated with single-strand specific nucleases (S1 nuclease for a DNA probe, or RNAses for an RNA probe). This results in digestion of the probe at all single- stranded areas: the extension beyond the mRNA sequences, and the single base- pair mismatch overlying the mutation (right). The radioactive digestion products are then separated by electrophoresis through a urea-containing polyacrylamide gel. The probe that annealed to normal, nonmutated mRNA is smaller than the undigested probe (by the length of the extended region not complementary to the mRNA) and will therefore migrate farther than undigested probe. The probe that annealed to the mutated mRNA will have been digested into two fragments whose summed length will equal that of the digested probe that annealed to nonmutated mRNA.


76 Ambion:

77 From: Gene Quantification Page by MW Pfaffl DNA MICROARRAY ANALYSIS

78 RNA extracted from a tumour is end-labelled with a fluorescent marker, then allowed to hybridise to a chip consisting of cDNAs or oligonucleotides. The precise location of RNA hybridisation to the chip can be determined using a laser scanner. Since the position of each unique cDNA or oligonucleotide is known, the presence of a cognate RNA for any given unique sequence can be determined.


80 MIAME Guidelines Minimum Information About a Microarray Experiment Provides a minimum standard that should be followed to objectively interpret findings from array experiments and ensure reproducibility of results Guidelines are provided for: Experimental design Samples used and preparation Hybridization techniques Microarray protocol Processing and Analysis of Data

81 Davidson University (Microarray Animation) Imagecyte (Microarray Animation) Microarray Data Analysis (Microarray Bibliography)

82 Why are they so different? Quantity or Quality?

83 (www)www


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