lecture_5 - Microarray Technology(Thinking carefully about...

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Microarray Technology (Thinking carefully about data) Lecture 5 6.874J/7.90J/6.807 David Gifford
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Microarrays can access in-vivo data derived from nucleic acid What kinds of information would we like to know? How do microarrays work? What kinds of errors are inherent in microarrays? How can we design measurement protocols to derive useful information using microarrays? mRNA expression is just one example of what we can observe Expression arrays are becoming less important over time
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The regulatory pathways that control gene expression programs are uncharted The mapping of transcriptional regulatory pathways will: • reveal how cell state, differentiation and response to stimuli are controlled • suggest new strategies to combat disease Transcriptional Regulatory Pathways
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Transcription of Protein-Coding Genes DNA-binding regulators occupy promoter elements ORF Jacob & Monod, 1961 Gilbert & Muller-Hill, 1967 Ptashne, 1967
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Transcription of Protein-Coding Genes DNA-binding regulators occupy promoter elements Histone H3 and H4 acetyl transferases and SWI/SNF recruited to promoter SAGA Nua4 SWI/SNF ORF ORF Peterson & Herskowitz, 1992 Brownell et al., 1996 Smith et al., 1998 Cosma et al., 1999 Reid et al., 2000 Bhanmik & Green, 2001 Larschan & Winston, 2001
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Transcription of Protein-Coding Genes DNA-binding regulators occupy promoter elements GTFs, Mediator, RNA polymerase II, and additional chromatin regulators recruited SAGA Nua4 Pol II Mediator GTFs SWI/SNF Isw1a ORF ORF ORF Reinberg & Roeder, 1987 Buratowski et al. 1989 Flores et al. 1992 Kolenske & Young, 1994 Kim & Kornberg, 1994 Li et al., 1999 Orphanides & Reinberg, 2002 Pokholok et al., 2002 Morillon et al., 2003 Histone H3 and H4 acetyl transferases and SWI/SNF recruited to promoter
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Transcription of Protein-Coding Genes DNA-binding regulators occupy promoter elements TFIIH phosphorylates RNA Pol II CTD on Ser5 Recruitment of Paf1 complex and Set1 histone H3 K4 methyl transferase SAGA Nua4 Pol II Mediator GTFs Set1 PAF1 SWI/SNF Isw1a ORF ORF ORF ORF Nislow et al., 1997 Briggs et al., 2001 Ng et al., 2003 Krogan et al., 2003 Histone H3 and H4 acetyl transferases and SWI/SNF recruited to promoter GTFs, Mediator, RNA polymerase II, and additional chromatin regulators recruited
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Transcription of Protein-Coding Genes DNA-binding regulators occupy promoter elements CTK1 phosphorylates RNA Pol II CTD on Ser2 Recruitment of Set2 H3 K36 methyl transferase and Isw1b SAGA Nua4 Pol II Mediator GTFs Set1 Set2 PAF1 SWI/SNF Isw1a ORF ORF ORF ORF ORF Isw1b Strahl et al., 2002; Krogan et al., 2003; Li et al., 2003 Histone H3 and H4 acetyl transferases and SWI/SNF recruited to promoter
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