1. CHMI 4226 - W20091 Recombinant DNA Technology CHMI 4226 E Week of Jan 23, 2009 Qualitative and quantitative methods for the analysis of gene expression

2. CHMI 4226 - W20092 cDNA clones! Ori C Amp R Sequencing Restriction mapping Sub-cloning Identification Expressed sequence tag (EST) mRNA expression Mutagenesis Complete? Blast probe 5’/3’ RACE

3. CHMI 4226 - W20093 Gene expression 5’ untranslated region (5’UTR): –located upstream of the ORF –Generally short (<150b) –Involved in the regulation of the initiation of translation Open reading frame (ORF): –The region of the mRNA encoding a specific protein –Sequence is well conserved across species 3’UTR: –Located downstream of the ORF –Generally quite long (>1000 b) –Involved in regulating mRNA stability as well as translation mRNA 5’UTRORF3’UTR AUG UAA UGA UAG

4. CHMI 4226 - W20094 Gene expression What would we like to know about our favorite mRNA? –Size of the mRNA (that actually matters…..) –Presence of alternative forms of the mRNA Inclusion/exclusion of specific exons or introns (may affect the integrity or coding potential of the ORF) Longer/shorter 5’UTR or 3’UTR (would affect translation efficiency or mRNA stability) –Expression levels During development Tissue-specificity Upon specific conditions (e.g. stress) Pathological situations –Which cells in a specific organ expresses our favorite mRNA

5. CHMI 4226 - W20095 Most widely used methods

6. CHMI 4226 - W20096 Northern Blot Qualitative Requires a nucleic acid probe Useful for: –Comparing the expression levels of a gene under different conditions –Determining the size of a particular mRNA –Identifying alternative forms of an mRNA (alternative splicing)

7. CHMI 4226 - W20097 Northern blot analysis RNA

8. CHMI 4226 - W20098 Northern Blot Analysis of tissue-specific expression Rate Thymus Prostate Testicule Utérus Petit intestin Colon Lymphocytes Rate Thymus Prostate Testicule Utérus Petit intestin Colon Lymphocytes

9. CHMI 4226 - W20099 Northern Blot

10. CHMI 4226 - W200910 Northern Blot – internal controls Detecting different levels of mRNA expression may be due to unequal RNA loading on the gel; To control for this possibility, the blot is also separately probed for a control mRNA, the expression of which does not change markedly under the conditions tested. Examples of control mRNAs: actin, GAPDH,  2-microglobulin Alternatively, a picture of the ethidium bromide-stained gel can be taken to visualize the rRNAs. The gel/autoradiogram can then be scanned, and the data represented as the signal intensity of the Favorite mRNA over the control.

11. CHMI 4226 - W200911 Northern Blot Detection of mRNA Induction

12. CHMI 4226 - W200912 Reverse transcription/PCR (RT-PCR)

13. CHMI 4226 - W200913 RT-PCR Steps: –1. RNA isolation –2. Conversion of mRNA into cDNA with reverse transcriptase –3. Amplification of the desired target by PCR Advantages: –Extremely sensitive, very simple and fast method to analyse gene expression; –Very little material is required ( ug for Northern); –Multiplexing is possible: amplification of several different targets in a single experiment; –Can yield quantitative data (i.e. # of mRNA molecules per cell). Drawbacks: –Too sensitive: false positives due to contamination is a real problem; –Obtaining quantitative data is difficult and requires a lot of optimization.

14. CHMI 4226 - W200914 PCR-Plateau effect http://www.biotechlab.northwestern.edu/pe/sld021.htm

15. CHMI 4226 - W200915 PCR-Plateau effect http://www.biotechlab.northwestern.edu/pe/sld021.htm

16. CHMI 4226 - W200916 PCR-Plateau effect Plateau Effect - The plateau effect is an attenuation of the normally exponential rate of product accumulation in a PCR reaction. It can be caused by: –depletion of dNTPs –depletion of primers –stability of the reactants (e.g. enzyme activity; particularly at the denaturation temperature) –end product inhibition by duplex DNA –non-specific competition for resources (production of incorrect product) –reannealing of specific products to one another instead of to the primers (this is particularly problematic when product concentration is high).

17. CHMI 4226 - W200917 PCR-Plateau effect http://www.biotechlab.northwestern.edu/pe/sld021.htm

18. CHMI 4226 - W200918 Semi-quantitative PCR In semi-quantitative PCR, the expression level of the favorite mRNA is expressed relative to an internal (part of the mRNA sample) or external (added for the PCR reaction) control. Problem: signal must be obtained during the linear phase of amplification.

19. CHMI 4226 - W200919 Semi-quantitative PCR GAPDH GADD45 GADD153 Culture Time 1 day 4 days 6 days 6 days -Gln +Gln 21 24 27 30 21 24 27 30

20. CHMI 4226 - W200920 Quantitative RT-PCR Competitive RT-PCR Problems with the use of controls for quantitative PCR: –Differences in amplification efficiency due to: Difference in size Difference in nucleotide composition Difference in primers used for amplification (different Tms, ect) –Don’t know the absolute amount of internal control in the reaction Mimick: –External control of known quantity –Size very similar to target (± 50 bp) –Same sequence as target –Uses same primers to amplify target and mimick –Mimick will compete with target during the amplification –Since we know the amount of mimick added to the reaction, we can get the absolute amount of the mRNA of interest in our sample.

21. CHMI 4226 - W200921 Competitive RT-PCR

22. CHMI 4226 - W200922 Real-Time PCR Makes use of fluorescent probes allowing us to monitor the progress of the PCR reaction IN REAL TIME (i.e. no need for agarose gel electrophoresis)... Major advantages: –Allows one to rapidly terminate the PCR experiment if something goes wrong; –Quantitative –Small volumes (microliter reactions): save a lot of $$$ Major disadvantages: –Instrumentation –Getting quantitative data is not trivial

23. CHMI 4226 - W200923 Real-Time PCR Technologies TaqMan technology SYBR Green technology

24. CHMI 4226 - W200924 Real-Time PCR Instrumentation

25. CHMI 4226 - W200925 Real-Time PCR The increase in fluorescence intensity is used to follow the progress of reaction. 10-fold dilutions of a DNA sample are amplified; The more DNA in the sample, the less cycles it takes to amplify it.

26. CHMI 4226 - W200926 Real-Time PCR Specificity is cheched by performing « melting curve » experiment with the final PCR product All PCR products are identical PCR product in « red » sample Is different than the others

27. CHMI 4226 - W200927 Real-Time PCR After the experiment, the data is examined for the PCR cycle at which a fluorescence signal above background is detected: this is called the cycle threshold, or C t ; Threshold Log scale C t = 22

28. CHMI 4226 - W200928 Real-Time PCR Quantification can be achieved by amplifying known amounts of a DNA sample, and using the data to graph a standard curve of the C t vs Log starting DNA concentration/ copy number; The amount of starting DNA in the unknown is then obtained using this standard curve; CtCt Threshold

29. CHMI 4226 - W200929 RNAse Protection Assay (RPA)

30. CHMI 4226 - W200930 RNAse Protection Assay (RPA) Involves the liquid hybridization of an RNA probe to an RNA sample (more efficient/quantitative than solid phase hybridization [Northern]); Unhybridized RNAs are degraded with a mixture of RNAses; the hybridized RNA probe is protected from RNAse action Protected RNA probe is then fractionnated by gel electrophoresis and visualized by autoradiography/phosphorimaging Quatification is possible by cutting the bands from the gel and counting the amount of radioactivity using a scintillation counter. Phosphorimager (pixels) CPMs (scintillation counter)

31. CHMI 4226 - W200931 RNAse Protection Assay (RPA) The RNA probe is prepared by in-vitro transcription of a cDNA molecule in the presence of [  32 P]UTP; The probe can be designed to contain regions of sequence divergence between different forms of an mRNA: simultaneous detection of several products of alternative splicing; Multiplexing is possible: several probes detecting different mRNAs can be mixed an used in a single tube (i.e. internal controls).

32. CHMI 4226 - W200932 RNAse Protection Assay (RPA)

33. CHMI 4226 - W200933 RNAse Protection Assay (RPA)

34. CHMI 4226 - W200934 Hybridation In-situ

35. CHMI 4226 - W200935 In-situ Hybridization Allows the detection of a specific mRNA in whole cells/tissues/organs/animals; The probe is labeled with either a radioisotope or a fluorescent dye, and hybridized to the material of interest; Novel imaging techniques allow scientists to obtain spectacular data!

36. CHMI 4226 - W200936 In-situ Hybridization

37. CHMI 4226 - W200937 In-situ Hybridization PNAS. 2003 100 (suppl. 1): 11836–11841

38. CHMI 4226 - W200938 In-situ Hybridization SCIENCE. 2004. 305: p846