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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
• Discussion of other possibile explanations of H
• Future work
• Acknowledgements
• References
Background of Olfactory
Receptors
Mouse
Human
Dog
OR
Pseudogenes
1500
900
838
20%
63%
18%
• 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.
Sample Olfactory Receptor
Locus: Mor28
40kb
150kb
Sakano et al. 2003
• Mouse and Human Model
• Conserved 1.6kb region
• Without the H region there is little or no
expression of ORs
Cis acting elements
Sakano 2003 4
• 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
Dot Plot: Human and Mouse
Human
Mouse
Pair view of Mouse and Human H
region aligned at a 85% threshold
Human
This diagram
shows the region
of similarity in the
dot plot. The area
of high
conservation is
about 300 base
pairs.
Mouse
Family Relations
Dot Plot 95% similiarity
Human
Mouse
Seeing that the
region of 300
basepairs was
well conserved
it became my
probe for
detecting new
H regions.
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
Science 2003
looked for the gene upstream
Unrooted evolutionary tree showing the
of the H region in mouse in
relationship of Mouse, Human, and Dog.
the dog genome.
The BLAST result of Mor28
Locus on the Dog Genome
Mor83
15: + 21643152
Mor28
21644049
15: - 21647887 21648782
Mor10
15: - 21647912
21648744
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
Mouse vs Human
Human chr14
Human vs Dog
Dog chr8
Mouse vs Human vs Dog
Mouse vs Dog
Another possibility
The 300 base pairs.
Mouse chr14:45,151,208-45,463,207
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.
References
1.
2.
3.
4.
5.
6.
7.
8.
9.
Buck L, Axel R. (1991) A novel multigene family may encode odorant
receptors: a molecular basis for odor recognition.Cell. 65, 175-87.
Galibert, F et al. (2003) Comparison of the canine and human olfactory
receptor gene repertoires.Genome Biology 4, 12
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.
Sakano, H. et al. (2003) Negative Feedback Regulation Ensures the One
Receptor–One Olfactory Neuron Rule in Mouse. Science. 302, 2088-2094.
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.
UCSC Genome Browser: http://genome.ucsc.edu
NCBI: www.ncbi.nlm.nih.gov
Ensembl: www.ensembl.org
Family Relations: http://cartwheel.caltech.edu