1. A Computational Analysis of the H Region of Mouse Olfactory Receptor Locus 28 Deanna Mendez SoCalBSI August 2004

2. Overview Background of olfactory receptors Introduce the H region as a possible cis regulatory element Define cis regulatory elements Results of looking for the H region Discussion of other possibile explanations of H Future work Acknowledgements References

3. Background of Olfactory Receptors A single odorant receptor gene is expressed by an olfactory neuron and that the axonal projections map to different glomeruli on the olfactory bulb. In 2003 a region of homology called the H region was identified as a putative cis regulatory element of the a particular set of olfactory receptors – MOR28 and their orthologous counterparts in humans. ORPseudogenes Mouse150020% Human90063% Dog83818%

4. Sample Olfactory Receptor Locus: Mor28 Mouse and Human Model Conserved 1.6kb region Without the H region there is little or no expression of ORs Sakano et al. 2003 40kb150kb

5. Cis acting elements A Cis acting elements are a sequence of DNA that can bind transcription factors and in so doing, control or modulate the level of transcriptional initiation from one or more nearby genes. 6 BLAST and Blat –whole genome view –across genome view Family Relations –local view of DNA Sakano 2003 4

6. Dot Plot: Human and Mouse Mouse Human

7. Pair view of Mouse and Human H region aligned at a 85% threshold Family Relations This diagram shows the region of similarity in the dot plot. The area of high conservation is about 300 base pairs. Human Mouse

8. Dot Plot 95% similiarity Seeing that the region of 300 basepairs was well conserved it became my probe for detecting new H regions. Mouse Human

9. Need for a node in the evolutionary Tree to obtain more general information Dog Genome was released, assembled, and made publically available in July 2004. To find an orthologous region in dog I used the three known olfactory receptors in mouse and blasted them to the dog genome and then looked for the gene upstream of the H region in mouse in the dog genome. Unrooted evolutionary tree showing the relationship of Mouse, Human, and Dog. Science 2003

10. Mor28 Mor10 Mor83 15: - 21647912 21648744 15: + 21643152 21644049 15: - 21647887 - 21648782 The BLAST result of Mor28 Locus on the Dog Genome

11. Orthologous Mor28 site in Dog

12. 2kb H region of mouse BLASTED on the dog genome Subject: 8 + 5474838 5474886 2kb

13. 300bp H region from Mouse(32) on Dog

14. Three way of comparison of Mouse, Human, and Dog Mouse chr14 Human chr14 Dog chr8 Mouse vs Human Human vs Dog Mouse vs Dog Mouse vs Human vs Dog

15. Another possibility Mouse chr14:45,151,208-45,463,207 The 300 base pairs.

16. Future Work Wet Experiment: Test the H region to see if it is a general enhancer. Dry experiments: Look at the other candidate homologous sequences

17. Acknowledgments Barbara Wold for giving me the opportunity to work in her lab and for her directing my work. Joe Roden for his time and enthusiasm for this project. Jamil Momand, Nancy Warter-Perez, Wendie Johnston, Sandra Sharp for making this program possible. Tim Ng and my fellow interns. NSF and NIH for funding this summer program.

18. References 1.Buck L, Axel R. (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition.Cell. 65, 175-87. 2.Galibert, F et al. (2003) Comparison of the canine and human olfactory receptor gene repertoires.Genome Biology 4, 12 3.Sakano, H. et al. (2001) Monoallelic expresion of the odourant receptor gene and axonal projection of olfactory sensory neurones. Genes to Cells. 6, 71-78. 4.Sakano, H. et al. (2003) Negative Feedback Regulation Ensures the One Receptor–One Olfactory Neuron Rule in Mouse. Science. 302, 2088-2094. 5.Kirkness E, Bafna V, Halpern A, Levy S, Remington K, Rusch D, Delcher A, Pop M, Wang W,Fraser C, Venter C. (2003) The Dog Genome: Survey Sequencing and Comparative Analysis. Science, 301, 1898-1903. 6.UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu 7.NCBI: www.ncbi.nlm.nih.govwww.ncbi.nlm.nih.gov 8.Ensembl: www.ensembl.orgwww.ensembl.org 9.Family Relations: http://cartwheel.caltech.eduhttp://cartwheel.caltech.edu