Case study reveals transcription factor (TF) modules, dynamic TF binding and an expanded role for cell cycle regulators
Mapping the DNA Damage Response
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
Overview of the approach
Overview of the approach
Overview of the approach
Transcription factors that regulate DNA damage response
Activated regulatory network
Transcription factors that regulate DNA damage response
TF knockout
“Deletion-buffered”
Activated regulatory network
Growth phenotype in MMS: mutants that display relative growth inhibition
Truncated Product Method (TPM): determine condition dependent binding
ChIP-chip of 30 TFs before and after DNA damage
YPD MMS+/-MMS
TPM
ChIP-chip Data Summary
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.
TFs may regulate different genes (bind different promoters) under different conditions.
Promoter regions analysisChIP-chip and DNA-Motif
TF-Knockout expression profiles:(look much like wild-type)
Environmental “epistasis analysis”:(deletion-buffering)
Deletion-buffering analysis
Bayesian Score
Deletion-buffering examples
RNR Genes are repressed by Rfx1p
Sensitive TFs are required for a greater number of damage responsive genes
Integrated model(regulatory paths explaining buffered genes)
Pathway reconstruction
Pathway reconstruction
Pathway reconstruction
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.
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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