The document discusses gene expression and various methods used to measure it. It describes how measuring mRNA levels can indicate which genes are actively being expressed in a cell. It provides details on transcription, regulatory elements that control it, and various techniques used to study gene expression, including microarray analysis, serial analysis of gene expression (SAGE), and northern blotting.

1. Gene Expression M.Tevfik DORAK http://www.dorak.info

2. 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

4. From: Gene Quantification Page by MW Pfaffl

5. 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 !

6. Transcribed and Nontranscribed Strands

7. From: Vlad Bajic at BioDiscovery Group, Singapore

10. Medical Biochemistry Pages http://www.indstate.edu/thcme/mwking/gene-regulation.html

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

13. University of Arizona Biology Project http://www.biology.arizona.edu/molecular_bio/molecular_bio.html

15. 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 Translation Broken-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

17. 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

20. Morey AK et al. JBC 1998 (http://www.biochemj.org/bj/330/1097/3301097.pdf) Chromosomal Location: 6p21.4 EDN1 Locus: ID 1906 EDN1 Genome Annotation (chromosome 6 reference genomic contig) : NT_007592 EDN1 Genomic Sequence (including the promoter region): J05005

21. EDN1 (GeneID 1906) GI: 340555 repeat_region 98...383 /rpt_family="Alu" protein_bind 739...745 /bound_moiety="acute phase reactant regulatory element" misc_feature 979..1039 /note="Z-DNA region; putative" protein_bind 2183..2188 /bound_moiety="acute phase reactant regulatory element" protein_bind 2951..2958 /bound_moiety="TPA/JUN" protein_bind 3241..3248 /bound_moiety="TPA/JUN" protein_bind 3316..3328 /bound_moiety="NF-1" protein_bind 3499..3505 /bound_moiety="TPA/JUN" CAAT_signal 3510..3515 /gene="EDN1" TATA_signal 3577..3582 /gene="EDN1" Exon 1 3608..3939 /gene="EDN1"

22. Regulatory SNPs

23. Medical Biochemistry Pages http://www.indstate.edu/thcme/mwking/rna.html

24. 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

25. Generating Protein Diversity from the “Small” Human Genome

26. Generating Protein Diversity from the “Small” Human Genome

30. Gene Expression in Prokaryotes Glick and Pasternak Fig. 3.10

31. Three kinds of RNA http://www.cu.lu/labext/rcms/cppe/traducti/tjpeg/trna.jpeg ; Tobin and Duschek, Asking About Life; http://www.tokyo-ed.ac.jp/genet/mutation/nort.gif 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

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

37. Transcription

39. Maston GA et al. 2006 ( www )

40. Maston GA et al. 2006 ( www )

41. Maston GA et al. 2006 ( www )

42. Maston GA et al. 2006 ( www )

43. Maston GA et al. 2006 ( www )

44. ( WWW )

56. 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

57. From: Weissmann & Lyko. BioTechniques 2003 EPIGENETIC CROSSTALK

58. Wellcome Trust http://www.wellcome.ac.uk/en/genome/thegenome/hg02b002.html

60. 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

63. Nigel Walker, NIEHS (www)

65. 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

66. Serial analysis of gene expression (SAGE) Page 169

67. SAGENet: http://www.sagenet.org/findings/index.html

69. DNA FOOTPRINTING ANALYSIS

70. RIBONUCLEASE PROTECTION ASSAY

71. 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.

73. Ambion: http://www.ambion.com/techlib/resources/miRNA/mirna_gen.html

74. From: Gene Quantification Page by MW Pfaffl DNA MICROARRAY ANALYSIS

75. DNA MICROARRAY ANALYSIS 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.

79. Why are they so different? Quantity or Quality?

80. ( www )