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Mapping the DNA Damage Response

Mapping the DNA Damage Response. Case study reveals transcription factor (TF) modules, dynamic TF binding and an expanded role for cell cycle regulators. Overview . Experimental factors and selection Multiple criteria used ChIP-on-chip Differential binding analysis

lysandra-cannon
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Mapping the DNA Damage Response

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  1. Mapping the DNA Damage Response Case study reveals transcription factor (TF) modules, dynamic TF binding and an expanded role for cell cycle regulators

  2. Overview • Experimental factors and selection • Multiple criteria used • ChIP-on-chip • Differential binding analysis • Gene expression of TF-deletion mutants • Clustering analysis • Deletion-buffering analysis • Data integration and pathway reconstruction

  3. Overview of the approach

  4. Overview of the approach

  5. Overview of the approach

  6. Transcription factors that regulate DNA damage response Activated regulatory network

  7. Transcription factors that regulate DNA damage response Activated regulatory network TF knockout “Deletion-buffered”

  8. Growth phenotype in MMS: mutants that display relative growth inhibition

  9. Truncated Product Method (TPM): determine condition dependent binding

  10. ChIP-chip of 30 TFs before and after DNA damage YPD MMS +/-MMS TPM

  11. ChIP-chip Data Summary TFs may regulate different genes (bind different promoters) under different conditions. Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways.Science. 2006 May 19;312(5776):1054-9.

  12. Promoter regions analysisChIP-chip and DNA-Motif

  13. TF-Knockout expression profiles:(look much like wild-type)

  14. Environmental “epistasis analysis”:(deletion-buffering)

  15. Deletion-buffering analysis Bayesian Score

  16. Deletion-buffering examples

  17. RNR Genes are repressed by Rfx1p

  18. Sensitive TFs are required for a greater number of damage responsive genes

  19. Integrated model(regulatory paths explaining buffered genes)

  20. Pathway reconstruction

  21. Pathway reconstruction

  22. Pathway reconstruction

  23. Integrated direct and indirect regulatory pathways (chIP-chip, prot-prot) that explain deletion-buffering relationships Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways.Science. 2006 May 19;312(5776):1054-9.

  24. Summary • “Sensitive” TFs control more of the DNA damage response than non-sensitive TFs • Regulatory networks are highly interconnected • Transcriptional regulation of important DNA damage checkpoint kinases are observed • Measuring differential TF-binding is difficult

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