a computational analysis of the h region of mouse olfactory receptor locus 28
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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 - PowerPoint PPT PresentationTRANSCRIPT
A Computational Analysis of the H Region of
Mouse Olfactory Receptor Locus 28
Deanna MendezSoCalBSI
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, 123. 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