A Computational Analysis of the H Region of

Mouse Olfactory Receptor Locus 28

Deanna Mendez

SoCalBSI

August 2004

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

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.

OR Pseudogenes

Mouse 1500 20%

Human 900 63%

Dog 838 18%

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

40kb 150kb

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

Dot Plot: Human and Mouse

Mouse

Human

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

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

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

Mor28

Mor10

Mor83

15: - 21647912 21648744

15: + 21643152 21644049

15: - 21647887 -21648782

The BLAST result of Mor28 Locus on the Dog Genome

Orthologous Mor28 site in Dog

2kb H region of mouse BLASTED on the dog genome

Subject: 8 + 5474838 5474886

2kb

2kb

300bp H region from Mouse(32) on Dog

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

Another possibility

Mouse chr14:45,151,208-45,463,207

The 300 base pairs.

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

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.

References1. 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.edu

7. NCBI: www.ncbi.nlm.nih.gov

8. Ensembl: www.ensembl.org

9. Family Relations: http://cartwheel.caltech.edu