Download MyoD Region - Cal State LA

Target Gene Predictions for
MyoD Genome-Wide
Dr. Barbara Wold’s Lab (Caltech)
Sean Caonguyen
SoCalBSI
8/15/2007
Outline
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Background
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Approach
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Cistematic Python Package
UCSC Genome Browser
Findings
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Regulation of Muscle Development
Chromatin Immunoprecipitation Sequencing (ChIPSeq)
RNA Sequencing (RNASeq)
Biological Significance
Distance from MyoD Regions and Peaks to closest Gene
Compare close genes to the expressed genes
Future Directions
Regulation of Muscle Development
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Why are Muscles
Important?
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For daily activities
To maintain biological
composition
TO LIVE!!
Myogenic Regulatory
Factors (MRFs)
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Myf 5
MyoD
Myogenin
Mrf 4
Early
http://files.myopera.com/honeybe/blog/wCars002%2520-%2520car%2520cartoon.jpg
Chromatin Immunoprecipitation
Sequencing (ChIPSeq)
MyoD
DNA
CHROMOSOMAL DNA
Each red box
denotes a
sequence read
Map sequence to genome
Johnson, D.S., et al. (2007)
and Fields, S. (2007)
Are the Close Genes Expressed?
Solexa
Nearby Genes
Genomic DNA
RNA Sequencing (RNASeq)
Introns
DNA
Exons
Transcription
5’ cap
Processing…
AAAAA
mRNA
AAAAA
Reverse
Transcription
DNA
Size Selected
Solexa/Illumina
Pre-mRNA
How are Genes Expressed?
Solexa/Illumina
Introns
Exons
Genomic DNA
Biological Significance of Analysis
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Help understand regulation for
the muscle network genes
Problems with Muscle Atrophy:
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Disuse of muscles
Aging
Zero Gravity
Study Muscular Dystrophy
Diseases
Improve drug development
Preventive care for genetic
diseases
Regulation is the key
http://cj_whitehound.madasafish.com/Rats_Nest/artwork/clipart/greenish_sick_rat_in_bed.gif
http://www.westyrell.com/lin/spaceman.gif
Location of Regulators
DNA
Gene C
Site
Gene A
Gene B
Approach to Project
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Tools
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Cistematic Python Package created by Ali Mortazavi
Data and Code from Ali Mortazavi and Qing Yuan
UCSC Genome Browser
Tasks
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Look at MyoD enriched regions
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Find distance to nearby genes
Determine which genes are expressed or suppressed
Find Neighborhood Genes
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Look for genes in 20kbp radius of the
MyoD sequence-tag-enriched regions
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Also determine distance to the peaks in
regions
MyoD Region
Gene
Gene
Gene
Gene
Gene
Gene
DNA
Hits at Peaks and in Regions
MyoD Region
Search by Peak or Region Midpoint?
5155 Genes
115 Genes
Region
5270 Genes
1635 Genes
Peak
∑ = 6905 Genes
6790 Genes
Contributions
Tools
Cistematic
Past Python Code
UCSC Genome Broswer
ChIP Seq
Find Genes within
20Kbp of Potential MyoD
Sites on the genome
RNA Seq
See if Expression
Level of Genes
Average
Findings
Future Directions
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Look at correlations of MyoD sites to distances to genes
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Potential regulation distances
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Isolated top hits for further analysis:
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Close
Far
Bidirectional
High
Mid
Low
Closer look at MyoD sites with no neighborhood gene
Reusable analysis for other proteins
Acknowledgements
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Mentor
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Wold Lab
Biological Investigators
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Jamil Momand
Sandy Sharp
Nancy Warter-Perez
Wendie Johnston
Funding by:
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DOE and NASA
NSF, NIH, and
Economic & Workforce
Development
Computational Gurus
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Brian Williams
Ali Mortazavi
SoCalBSI Faculty and staff
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Barbara Wold
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Diane Trout
Brandon King
Cory Tobin
Fellow Colleagues
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Qing Yuan
Herbert Lee