1 / 43

Junguk Hur School of Informatics & Center for Genomics and Bioinformatics

Characterization of transcriptional responses to environmental stress by differential location analysis. Junguk Hur School of Informatics & Center for Genomics and Bioinformatics. Indiana University Bloomington, IN. OVERVIEW. Overview. Background / Motivation

kato-witt
Download Presentation

Junguk Hur School of Informatics & Center for Genomics and Bioinformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Characterization of transcriptional responses to environmental stress by differential location analysis Junguk HurSchool of Informatics & Center for Genomics and Bioinformatics Indiana University Bloomington, IN

  2. OVERVIEW Overview • Background / Motivation • Location Analysis / Differential Binding • TF Response Classification • Comparison with Microarray • Conclusion / Future Work Capstone Presentation Junguk Hur

  3. Central Dogma Overview Background http://campus.queens.edu/faculty/jannr/bio103/tests/TEST2Help.htm Capstone Presentation Junguk Hur

  4. Transcriptional Regulation Overview Background Albert et al., Molecular Cell Biology of the Cell Capstone Presentation Junguk Hur

  5. Transcription Factors Transcriptional Regulation Overview Background Capstone Presentation Junguk Hur

  6. Response to Environment Overview Background Broach et al. Curr Opin Microbiol 2004 Capstone Presentation Junguk Hur

  7. High-throughput DNA Microarray – mRNA expression http://www.fao.org/DOCREP/003/X6884E/x6884e03.htm Previous Studies - Expression Overview Background Capstone Presentation Junguk Hur

  8. Previous Studies - Expression Overview Background • 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 Capstone Presentation Junguk Hur

  9. Previous Studies – ChIP-Chip Overview Background Which genes are directly regulated by TFs? (Environment specific use of regulatory code) Harbison et al. Nature 2004 Capstone Presentation Junguk Hur

  10. Motivation and Goal Overview Background • Limitation of Microarray data for understanding regulatory system upon environmental change • Previous qualitative analysis of ChIP-Chip • Integration of heterogeneous dataChIP-Chip (direct regulation) + Microarray (direct/indirect regulation) • Quantitative analysis of TF binding • Better understanding of differential responsesof transcriptional regulatory system via differential location analysis Capstone Presentation Junguk Hur

  11. Location Analysis Overview Background 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 Capstone Presentation Junguk Hur

  12. Differential Location Analysis Overview Background 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) Capstone Presentation Junguk Hur

  13. Data Sets - I Overview Background Location Analysis • ChIP-on-Chip • 204 Yeast Transcription Factors (TFs)1 • 1 rich medium condition + 13 stress conditions • 6540 genes & corresponding promoter sequences. • Microarray Capstone Presentation Junguk Hur

  14. 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 Data Sets - II Overview Background Location Analysis Capstone Presentation Junguk Hur

  15. Increased binding in stress condition Decreased binding in stress condition Differential Binding Ratio Overview Background Location Analysis Differential Binding Rich medium Stress Condition How different the binding ratio btw different conditions??? Capstone Presentation Junguk Hur

  16. Ai, Bi: binding ratio of TF k to regulated region iunder stress and rich medium culture condition respectively -1 Pik 1 Rich medium Stress Condition PiK > 0 UP PiK< 0 DOWN Differential Binding Measure Overview Background Location Analysis Differential Binding Differential binding is represented as Pik by using ChIP-chip binding ratio data between stress condition (A) and rich medium (B). Capstone Presentation Junguk Hur

  17. High-confidence Binding Data (p0.001) All ChIP-Chip Binding Data Normal distribution Skewed to negative direction Distribution of Pik - I Overview Background Location Analysis Differential Binding Ex) FHL1 YPD (Rich Medium) vs SM (Amino acid starvation) Capstone Presentation Junguk Hur

  18. Distribution of Pik - II Overview Background Location Analysis Differential Binding • Number of UP/DOWN differentially bound regions (genes) for each TF-cond pair • High-confidence data point only (p<0.001) -1 Pik 1 0.5  |Pik| 1 Capstone Presentation Junguk Hur

  19. Chi-Square Test - I Overview Background Location Analysis Differential Binding * Chi-Square tests for Pikof 147 TF-condition pairs to check their distributions (Normal or skewed) * R-package & Perl scripts * P<0.05  Skewed distribution High-confidence Binding Data (p0.001) All ChIP-Chip Binding Data Skewed Dist. (p=0.00003) Normal Dist. (p=0.97) Capstone Presentation Junguk Hur

  20. Chi-Square Test - II Overview Background Location Analysis Differential Binding Skewed Distribution Chi-square test : p < 0.05 105 TF-Cond pairs (out of 147) : 70% Capstone Presentation Junguk Hur

  21. Classification of TFs - I Overview Background Location Analysis Differential Binding TF response classification Depending on patterns of the skewed pattern , 105 TF-condition pairs have been grouped into three categories. UP : More than 2/3 are in ‘+’ direction DOWN : More than 2/3 are in ‘–’ direction BOTH : Similar proportions of ‘+’ and ’-’ Capstone Presentation Junguk Hur

  22. Classification of TFs - II Overview Background Location Analysis Differential Binding TF response classification UP : YAP5_H2O2Hi DOWN : SFP1_H2O2Lo BOTH : HPO4_Pi Capstone Presentation Junguk Hur

  23. Differential Location Analysis - Summary Overview Background Location Analysis Differential Binding TF response classification • Comparison of TF binding between rich medium and stress cond. • Represented by PiK • Distribution of PiK • Normal and Skewed • Chi-Square Tests • 70% TF-cond pairs  differential distribution • Classification of TF responses • UP, DOWN, and BOTH Capstone Presentation Junguk Hur

  24. How differential binding? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Changes in the TF expression Changes in the TF expression Different TFBS signature for different category Interaction with other TFs expression Modifications in TFs (protein level) Changes in physical structures (epigenetic features) Other unknown reasons Capstone Presentation Junguk Hur

  25. Comparison with Microarray - I Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray ChIP-Chip vs Microarray data ---------------------- expression levels of transcription factors (TFs). ---------------------- H2O2 Low (oxidation) ---------------------- TF-Cond pairs : 28 Skewed : 23 Normal : 5 Capstone Presentation Junguk Hur

  26. Comparison with Microarray - II Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray SM (Sulfometuron methyl)Amino acid starvation -------------------------- ChIP-Chip 0.2 g/ml final 2 hours -------------------------- Microarray 0.2 g/ml 15 minutes 5.0 g/ml4 hours -------------------------- TF-Cond pairs : 34 Skewed : 21 Normal : 13 Capstone Presentation Junguk Hur

  27. Comparison with Microarray - III Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray H2O2 Oxidation stress SM (Sulfometuron methyl) Amino acid starvation Capstone Presentation Junguk Hur

  28. Comparison with Microarray - IV Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray 50~60%of differentially binding TFs have NO significant expression change Changes of gene regulation (differential binding) cannot be fully revealed by Microarray Capstone Presentation Junguk Hur

  29. How differential binding? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Changes in the TF expression Different TFBS signature for different category Interaction with other TFs expression Modifications in TFs (protein level) Changes in physical structures (epigenetic features) Other unknown reasons Capstone Presentation Junguk Hur

  30. Conclusion Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Conclusion / Future Work • Categorization of Transcription Factors (TFs) depending on the responses to stress • No significant expression changes in about 50% of the tested TFs in response to environmental changes. • Importance of integrating differential binding of TFs with gene expression to get the bigger picture Capstone Presentation Junguk Hur

  31. Diff. Expression Diff. Location Integration Diff. Proteomics (open) Diff. Protein-Protein Int. (open) Future Work Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. TF-TF Corr. Conclusion / Future Work • Investigating the biological mechanism of the differentially binding of TFs • Target gene of expression level • Post-translational modification • Protein-protein interaction • Comprehensive differential analysis Capstone Presentation Junguk Hur

  32. References Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. TF-TF Corr. Conclusion / Future Work • Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104. . • 2. Shapira, M., E. Segal, and D. Botstein, Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell, 2004. 15(12): p. 5659-69. • 3. Gasch, A.P., et al., Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell, 2000. 11(12): p. 4241-57. • 4. Causton, H.C., et al., Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell, 2001. 12(2): p. 323-37. • 5. Jia, M.H., et al., Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol Genomics, 2000. 3(2): p. 83-92. Capstone Presentation Junguk Hur

  33. Acknowledgements Dr. Haixu Tang Dr. Sun Kim Dr. Mehmet Dalkilic Dr. Predrag Radivojac Seung-hee Bae Sourav Roy Capstone class 2006 School of informatics Center for Genomics and Bioinformatics Dr. Zhixiong Xue at DuPont My Family Capstone Presentation Junguk Hur

  34. Thank you Capstone Presentation Junguk Hur

  35. Thank you Capstone Presentation Junguk Hur

  36. Thank you Capstone Presentation Junguk Hur

  37. How differential binding? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. Different TFBS signature for different category Changes in the TF expression Different TFBS signature for different category Interaction with other TFs expression Modifications in TFs (protein level) Changes in physical structures (epigenetic features) Other unknown reasons Capstone Presentation Junguk Hur

  38. Different TFBS signatures? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. • Category “BOTH” has similar numbers of Up-differentially bound and Down-differentially bound regions. • Is there any difference between these TFBSs in different groups? Capstone Presentation Junguk Hur

  39. BOTH Up seqs Down seqs Step1 TFBSs TFBSs Step2 Profile Profile Step3 Different TFBS signatures? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. Step1. Collect putative TFBS A. Frankel’s motifs (102TFs) B. Gary Stormo’s “Patser” Step2. Create profiles from collected TFBS seqs Step3. Profile comparison A. “MatCompare” program by Michale Zhang Capstone Presentation Junguk Hur

  40. Different TFBS signatures? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. High-Threshold Capstone Presentation Junguk Hur

  41. Different TFBS signatures? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. Low-Threshold Capstone Presentation Junguk Hur

  42. How differential binding? Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. TF-TF Corr. Association with other TFs Changes in the TF expression Different TFBS signature for different category Association with other TFs Modifications in TFs (protein level) Changes in physical structures (epigenetic features) Other unknown reasons Capstone Presentation Junguk Hur

  43. TF-TF Correlation Overview Background Location Analysis Differential Binding TF Response Classification Comp. with Microarray Diff. Binding Motif Anal. TF-TF Corr. TF TF Capstone Presentation Junguk Hur

More Related