Indiana University Bloomington, IN Junguk Hur School of Informatics & Center for Genomics and Bioinformatics Characterization of transcriptional responses to environmental stress by differential location analysis Capstone Presentation Junguk Hur OVERVIEW Background / Motivation Location Analysis / Differential Binding TF Response Classification Comparison with Microarray Conclusion / Future Work Overview Capstone Presentation Junguk Hur Central DogmaOverview Background Capstone Presentation Junguk Hur Transcriptional Regulation Albert et al., Molecular Cell Biology of the Cell Overview Background Capstone Presentation Junguk Hur Transcriptional Regulation Overview Background Transcription Factors Capstone Presentation Junguk Hur Response to Environment Overview Background Broach et al. Curr Opin Microbiol 2004 Capstone Presentation Junguk Hur Previous Studies - ExpressionHigh-throughput DNA Microarray mRNA expression Overview Background Capstone Presentation Junguk Hur Previous Studies - Expression Literature : Gene Expression Microarray Stress Exploring the metabolic and genetic control of gene expression on a genomic scale, DeRisi JL, et al. (1997) Science Genomic expression programs in the response of yeast cells to environmental changes, Gasch AP, et al. (2000) Mol Biol Cell Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source, Kuhn KM, et al. (2001) Mol Cell Biol Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae, Carmel-Harel O, et al. (2001) Mol Microbiol Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces cerevisiae, Shakoury-Elizeh M, et al. (2004). Mol Biol Cell Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source, Ronen M and Botstein D (2005) Proc Natl Acad Sci About 900 publications Overview Background Capstone Presentation Junguk Hur Previous Studies ChIP-Chip Which genes are directly regulated by TFs? Harbison et al. Nature 2004 Overview Background (Environment specific use of regulatory code) Capstone Presentation Junguk Hur Motivation and Goal Limitation of Microarray data for understanding regulatory system upon environmental change Previous qualitative analysis of ChIP-Chip Integration of heterogeneous data ChIP-Chip (direct regulation) + Microarray (direct/indirect regulation) Quantitative analysis of TF binding Better understanding of differential responses of transcriptional regulatory system via differential location analysis Overview Background Capstone Presentation Junguk Hur Location Analysis Genome-wide Location Analysis : ChIP-on-Chip Exp. In vivo assay based on ChIP (Chromatin Immuno-Precipitation) High-throughput array experiment Where and how strongly TF binds to Overview Background Location Analysis Capstone Presentation Junguk Hur Differential Location Analysis Harbison et al. Nature 2004 Saccharomyces cerevisiae (budding yeast) 204 TFs in 14 conditions (352 experiments) Genome-wide location data (11,000 interactions) Overview Background Location Analysis Capstone Presentation Junguk Hur ChIP-on-Chip 204 Yeast Transcription Factors (TFs) 1 1 rich medium condition + 13 stress conditions 6540 genes & corresponding promoter sequences. Microarray Stress ConditionConcentrationTime pointArrayRef. H2O2 oxidation0.3 mM20 minscDNA2 H2O2 oxidation0.32 mM20 minscDNA3 H2O2 - oxidation0.4 mM20 minsoligo4 SM (Sulfometuron methyl) AA starvation 0.2 g/ml 15 minscDNA5 SM (Sulfometuron methyl) AA starvation 0.2 g/ml 240 minscDNA5 Data Sets - I Overview Background Location Analysis Capstone Presentation Junguk Hur Data Sets - II ChIP-on-Chip Data Preprocessing P-value and ratio data from Harbison et al. NaN point removal Ratio value below 1 set to 1 Stress conditions 13 stress conditions 147 TF-cond pairs Overview Background Location Analysis Capstone Presentation Junguk Hur Differential Binding Ratio Rich mediumStress Condition Increased binding in stress condition Decreased binding in stress condition How different the binding ratio btw different conditions??? Overview Background Location Analysis Differential Binding Capstone Presentation Junguk Hur Differential Binding Measure A i, B i : binding ratio of TF k to regulated region i under stress and rich medium culture condition respectively -1 P i k 1 Differential binding is represented as P i k by using ChIP-chip binding ratio data between stress condition (A) and rich medium (B). Overview Background Location Analysis Differential Binding Rich mediumStress Condition P i K > 0 UP P i K < 0 DOWN Capstone Presentation Junguk Hur All ChIP-Chip Binding Data Normal distribution Distribution of P i k - I Ex) FHL1 YPD (Rich Medium) vs SM (Amino acid starvation) High-confidence Binding Data (p 0.001) Skewed to negative direction Overview Background Location Analysis Differential Binding Capstone Presentation Junguk Hur Distribution of P i k - II Number of UP/DOWN differentially bound regions (genes) for each TF-cond pair High-confidence data point only (p