1. Biochemistry 412 2005 5 April Lecture DNA Microarrays

2. Microarrays DNA Arrays Protein Arrays Other

3. Microarrays DNA Arrays Protein Arrays Other

4. Stolovitky (2003) Curr. Opin. Struct. Biol. 13, 370. Microarrays Have Led to an Explosion in mRNA Profiling Studies

5. Grünenfelder & Winzeler (2002) Nature Rev. Genet. 3, 653. Two Main Types of DNA Microarrays

6. Lockhart & Winzeler (2000) Nature 405, 827.

7. Pease et al (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 5022. Note: 4N masks required to make an array of oligonucleotides, each of length N. Affymetrix Gene Chips - In Situ Synthesis

8. Pease et al (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 5022. Note: this is the photolabile blocking group, “X”, indicated schematically in Figure 1.

9. Lipshutz et al (1999) Nature Genet. (suppl.) 21, 20. Key feature: known oligo sequence at each “address” on the chip.

10. In situ synthesized (Affymetrix) microarrays: Advantage - massive coverage of sequences possible Disadvantage - expensive and not easily customized Spotted arrays (oligonucleotides or dsDNA): Advantage - flexibility and cost; can be “home-made” Disadvantage - big initial investment; less standardization

11. Note: Not all arrays have to be on chips…! - Illumina, Inc.

12. Caveat….Caveat….Caveat…!! Results from the different DNA microarray methods don’t always agree! And results for mRNA abundance differences don’t always agree with protein abundance data!

13. Stages in the Life Cycle of a Technological Innovation 1. Unveiling (first publication) 2. Hype (lots of follow-on publications, meetings, venture capital, etc.) 3. Disillusionment (more paper opportunities!) 4. Promise eventually fulfilled (years later) 5. Enters routine use

14. Applications of DNA Microarrays Genotyping mRNA profiling and “transcriptome” analysis Genome analysis (cancer and evolutionary studies) Genome-wide splicing analyses Etc.

15. Applications of DNA Microarrays Genotyping mRNA profiling and “transcriptome” analysis Genome analysis (cancer and evolutionary studies) Genome-wide splicing analyses Etc.

16. Comparative mRNA Analyses Using Microarrays Bryant et al (2004) Lancet Infect. Disease 4, 100.

17. Technical Proficiency & Experimental Design are Key to Reproducibility Lockhart & Barlow (2001) Nature Rev. Neurosci. 2, 63.

18. However, if your technique isn’t good enough, the data must be “normalized”... Forster et al (2003) J. Endocrinol. 178, 195.

19. Microarray data: Analysis of a hypothetical time course of mRNA abundances for several genes Leung & Cavalieri (2003) Trends in Genetics 19, 649.

20. Ref: Lee et al (1999) Science 285, 1390. Note: caloric restriction gene chip experiment w/ rats.

21. Lee et al (1999) Science 285, 1390.

22. Huang et al (2001) Science 294, 870. Common Genes Induced in Immature Dendritic Cells in Response to Infection with Diverse Pathogens

23. Bassett et al (1999) Nature Genet. (suppl.) 21, 51.

24. Applications of DNA Microarrays Genotyping mRNA profiling and “transcriptome” analysis Genome analysis (cancer and evolutionary studies) Genome-wide splicing analyses Etc.

25. Microarrys Can Also be Used to Analyze Chromosomal Rearrangments Albertson & Pinkel (2003) Human Molec. Genet. 12, R145. CGH - “Comparative genomce hybridization LOH - “Loss of heterozygosity”

27. Applications of DNA Microarrays Genotyping mRNA profiling and “transcriptome” analysis Genome analysis (cancer and evolutionary studies) Genome-wide splicing analyses Etc.

28. Microarrays can be used to detect tissue-specific alternative splicing Blue - tissue 1 Purple - tissue 2 Yellow - pooled sample (average) Le et al (2004) Nucleic Acids Research 32, e180.

29. Microarray probe elements specifically designed to detect alternative splicing Barrass & Beggs (2003) Trends in Genetics 19, 295.

30. Applications of DNA Microarrays Genotyping mRNA profiling and “transcriptome” analysis Genome analysis (cancer and evolutionary studies) Genome-wide splicing analyses Etc.

31. RNA as a repository of past generations’ genetic information?? Weigel & Jürgens (2005) Nature 434, 443.