1. Effect of polymorphisms on transcriptional regulation in mice
Preliminary study of SNPs in the promoter region of genes with strong cis-eQTL
Manish Anand
Advisors: Dr. Debraj GuhaThakurta, Dr. Sun Kim
ROSETTA INPHARMATICS, and INDIANA UNIVERSITY
24th Sep, 2004

2. Overview Background Methods Results Conclusions
TFBS predictions genome-wide
TF specific analysis
Motifs in Promoter Regions
Results
Conclusions

3. Background

4. Central dogma ZOOM IN tRNA transcription DNA rRNA snRNA translation
POLYPEPTIDE
mRNA

5. Transcription – key steps
Initiation
Elongation
Termination
DNA

6. Transcription – key steps
Initiation
Elongation
Termination
DNA

7. Transcription – key steps
Initiation
Elongation
Termination
DNA
DNA +
RNA

8. Methods

9. Regulation of Genes Transcription Factor RNA polymerase DNA
Coding region
Regulatory Element

10. Gene
Upstream region (-0.5/1/5Kb)
SNP

11. SNP
Gene 1
SNP
Gene 2
SNP
Gene 3

12. SNPs
Upstream 1
Upstream 2
Upstream 3
Upstream 4
TF predictions

13. Selected Predictions

14. T G T C A A A G

15. PATSER / MATCH SCORE = 0.95 T
PATSER / MATCH SCORE = 0.22 A

16. TF T
0.95 TF
0.22 A

17. T Gene Expression A Gene Expression
Mice images taken from Terry Speed’s lecture ‘How many genes? Mapping mouse traits, January 20, 2004’

18. Consequences of point mutations in the promoter
for the b-globin gene
(From T. Maniatis, S. Goodbourn, and J. A. Fischer, Science 236, 1987, 1237.)

19. TFBS Predictions Analysis

20. General Summary

21. MATCH Score Difference Analysis

22. TF specific analysis

23. Motifs whose predicted binding sites are disrupted (show score differences)

24. Motifs whose predicted binding sites are disrupted (site drops)

25. MOTIF DISCOVERY

26. Novel MOTIFs in positive set

27. MOTIFs in negative set

28. Future Investigations

29. Future Investigations
Mapping of real (experimentally verified) binding sites in TRANSFAC onto the genome
Observing whether SNPs that disrupt these binding sites are in gene regions that show strong cis-acting eQTLs.
Selection of several genes that show strong cis-eQTLs and have either real or predicted transcription factor binding sites disrupted in their upstream regions for experimental follow-up/validation with genotyping and measurement of expressions with different variants observed in the different strains of mice.
Such experiments would help in identification of causal variants for expression changes in these genes.

30. Conclusions

31. Conclusions
Amongst genes with cis-eQTLs, more genes have polymorphisms in their promoter regions
Significantly more genes in the set with cis-acting eQTLs show score differences in putative TFBSs compared to control set
Identification of specific TFs whose binding site predictions are disrupted in genes with cis-acting eQTLs
Identification of novel DNA motifs around SNP regions in the positive set

32. Acknowledgements Rosetta Inpharmatics Indiana University
Dr. Debraj GuhaThakurta
Dr. Eric Schadt
Dr. John Lamb
Dr. Stephen Edwards
Dr. Barmak Modrek
Indiana University
Dr. Sun Kim
Dr. Gary Wiggins
Dr. Marty Siegel
Few images were taken from ‘Basic Biology for CS262’ - OMKAR DESHPANDE, Stanford University