1. What is the Best Way to Find the Binding Site for a Transcription Factor?
Dennis Shasha, Courant Institute, New York University
With
Philip Benfey and Ken Birnbaum Biology Department,
New York University.

2. Transcriptional Networks
Induction
Specificity
Modularity
AAAA
AAAA
AAAA
e.g. cis-element
AAAA
AAAA
Repression
AAAA
AAAA
AAAA
AAAA
Time 1
Time 2
Time 3

3. Genomic and Expression Data
Cis-regulatory regions of expressed genes
Expres-sion Level
Time

4. Clusters of Co-Expressed Genes
Expres-sion level
Time a a a a a a a a a
Over-represented motifs

5. Low Correlation Expression Level Time Time Transcription Factor
Dowstream Genes

6. Modularity From: Arnone & Davidson, Development, 1997
later expression module
early specification module
From: Arnone & Davidson, Development, 1997

7. Transcription Factor X
Expres-sion
Time
NAAAAAA.. ..TTTTTTN

8. Time Expres-sion Gene Cis - regulatory region A Transcription Factor X
Expression levels of genes with ACA?GTC in their promoters
Time
Gene
Cis -
regulatory
region
ACA?GTC A

9. Time Expres-sion Gene Cis - regulatory region A B
Transcription Factor X
Expres-sion
Expression levels of genes with ACA?GTC in their promoters
Time
Gene
Cis -
regulatory
region
ACA?GTC A
ACA?GTC B

10. Time Expres-sion Gene Cis - regulatory region A B C
Transcription Factor X
Expres-sion
Expression levels of genes with ACA?GTC in their promoters
Time
Gene
Cis -
regulatory
region
ACA?GTC A
ACA?GTC B
ACA?GTC C

11. Composite expression of ACAGTC at Time 5
Transcription Factor X
Expres-sion
Expression levels of genes with ACA?GTC in their promoters
Time
Gene
Cis -
Expression
regulatory
Level
Example: Time 5
region
ACA?GTC A 2
ACA?GTC B 4
ACA?GTC C 2
= 8
Composite expression of ACAGTC at Time 5

12. Composite expression of ACAGTC at Time 5
Transcription Factor X
Composite expression of genes with ACA?GTC in promoter
Expres-sion
Time
Expression levels of genes with ACA?GTC in their promoters
Gene
Cis -
Expression
regulatory
Level
Example: Time 5
region
ACA?GTC A 2
ACA?GTC B 4
ACA?GTC C 2
= 8
Composite expression of ACAGTC at Time 5

13. Cooperative Binding Model
TFs
AND
Binding Sites
TF Expression
Cell Type A
Cell Type B
Cell Type C Z Z
Expression Level A B C Z

14. X Cooperative Binding Model TFs AND Binding Sites TF Expression
Cell Type A
Cell Type B
Cell Type C X Z
Expression Level A B C
Target Gene Expression
Expression Level A B C

15. X X X X Cooperative Binding Model TFs AND Binding Sites TF Expression
Cell Type A
Cell Type B
Cell Type C Z Z
Expression Level A B C Z Z X X
Target Gene Expression Z Z Z Z Z X
Expression Level X A B C

16. X X X X Cooperative Binding Model TFs AND Binding Sites TF Expression
Cell Type A
Cell Type B
Cell Type C Z Z
Expression Level A B C Z Z X X
Target Gene Expression Z Z Z Z Z X
Expression Level X A B C

17. Cooperative Binding Model
TFs OR
Binding Sites

18. Independent Binding Model: well handled by Bussemaker et al.

19. Assumptions: TF RNA Expression = TF protein (protein movement)
TFs are active where they are expressed (co-factors)
Binding sites are within 2 kb of initiation site

20. Testing the Method Yeast Fully sequenced genome
Genome-wide mRNA expression profiles
300 knockout lines from Rosetta (Hughes et al. 2000)
2 datasets on yeast progressing through the cell cycle (Spellman et al. 1998; Cho et al. 1998)

21. Results for STE12 *From SCPD (Zhang, Cold Spring Harbor)
Dennis, the point of the lower
*From SCPD (Zhang, Cold Spring Harbor)

22. Results for STE12 *From SCPD (Zhang, Cold Spring Harbor)
Dennis, the point of the lower
*From SCPD (Zhang, Cold Spring Harbor)

23. Results for STE12 *From SCPD (Zhang, Cold Spring Harbor)
Dennis, the point of the lower
*From SCPD (Zhang, Cold Spring Harbor)

24. Overall Results

25. Conclusions
Technique: correlate transcription factor expression with cis-element expression. Can capture information that would be missed by gene expression correlation.
Can handle cooperative (AND) and independent (OR) cases. Does less well for complex circuits.
Future effort: manipulate promoters to eliminate false positives. (Information theory + experiments)