target gene predictions for myod genome-wide dr. barbara wold’s lab (caltech)
DESCRIPTION
Target Gene Predictions for MyoD Genome-Wide Dr. Barbara Wold’s Lab (Caltech). Sean Caonguyen SoCalBSI 8/15/2007. Outline. Background Regulation of Muscle Development Chromatin Immunoprecipitation Sequencing (ChIPSeq) RNA Sequencing (RNASeq) Biological Significance Approach - PowerPoint PPT PresentationTRANSCRIPT
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Target Gene Predictions for Target Gene Predictions for MyoD Genome-Wide MyoD Genome-Wide Dr. Barbara Wold’s Lab (Caltech)Dr. Barbara Wold’s Lab (Caltech)
Sean CaonguyenSean CaonguyenSoCalBSI SoCalBSI 8/15/20078/15/2007
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OutlineOutline BackgroundBackground
Regulation of Muscle DevelopmentRegulation of Muscle Development Chromatin Immunoprecipitation Sequencing (ChIPSeq)Chromatin Immunoprecipitation Sequencing (ChIPSeq) RNA Sequencing (RNASeq) RNA Sequencing (RNASeq) Biological SignificanceBiological Significance
ApproachApproach Cistematic Python PackageCistematic Python Package UCSC Genome BrowserUCSC Genome Browser
FindingsFindings Distance from MyoD Regions and Peaks to closest GeneDistance from MyoD Regions and Peaks to closest Gene Compare close genes to the expressed genesCompare close genes to the expressed genes
Future DirectionsFuture Directions
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Regulation of Muscle Regulation of Muscle DevelopmentDevelopment
Why are Muscles Why are Muscles Important?Important? For daily activitiesFor daily activities To maintain biological To maintain biological
compositioncomposition TO LIVE!! TO LIVE!!
Myogenic Regulatory Myogenic Regulatory Factors (MRFs)Factors (MRFs) Myf 5Myf 5 MyoDMyoD MyogeninMyogenin Mrf 4Mrf 4
Early
http://files.myopera.com/honeybe/blog/wCars002%2520-%2520car%2520cartoon.jpg
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MyoD
Johnson, D.S., et al. (2007) Johnson, D.S., et al. (2007) and Fields, S. (2007)and Fields, S. (2007)
DNA
CHROMOSOMAL DNA
Map sequence to genome
Each red boxdenotes asequence read
Chromatin Chromatin Immunoprecipitation Immunoprecipitation Sequencing (ChIPSeq)Sequencing (ChIPSeq)
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Are the Close Genes Are the Close Genes Expressed?Expressed?
Genomic DNA
Nearby GenesNearby Genes
Solexa
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RNA Sequencing (RNASeq)RNA Sequencing (RNASeq)
Introns ExonsExons
AAAAA Pre-mRNAAAAAA mRNA5’ cap
Reverse Transcription
DNA
Solexa/Illumina
Size Selected
DNA
TranscriptionProcessing…
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How are Genes Expressed?How are Genes Expressed?
Genomic DNA
Introns ExonsExons
Solexa/Illumina
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Biological Significance of AnalysisBiological Significance of Analysis
Help understand regulation Help understand regulation for the muscle network for the muscle network genesgenes
Problems with Muscle Problems with Muscle Atrophy:Atrophy: Disuse of musclesDisuse of muscles AgingAging Zero GravityZero Gravity
Study Muscular Dystrophy Study Muscular Dystrophy DiseasesDiseases
Improve drug development Improve drug development Preventive care for genetic Preventive care for genetic
diseasesdiseasesRegulation Regulation is the is the keykey
http://cj_whitehound.madasafish.com/Rats_Nest/artwork/clipart/greenish_sick_rat_in_bed.gif
http://www.westyrell.com/lin/spaceman.gif
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Location of RegulatorsLocation of Regulators
Gene A Gene BGene CDNASite
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Approach to ProjectApproach to Project
ToolsTools Cistematic Python Package created by Cistematic Python Package created by Ali MortazaviAli Mortazavi Data and Code from Ali Mortazavi and Qing YuanData and Code from Ali Mortazavi and Qing Yuan UCSC Genome BrowserUCSC Genome Browser
TasksTasks Look at MyoD enriched regionsLook at MyoD enriched regions
Find distance to nearby genes Find distance to nearby genes Determine which genes are expressed or suppressedDetermine which genes are expressed or suppressed
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Find Neighborhood GenesFind Neighborhood Genes
Look for genes in 20kbp radius of Look for genes in 20kbp radius of the MyoD sequence-tag-enriched the MyoD sequence-tag-enriched regionsregions Also determine distance to the peaks Also determine distance to the peaks
in regionsin regions
DNA
MyoD Region
Gene GeneGene GeneGeneGene
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Hits at Hits at PeaksPeaks and in and in RegionsRegions
MyoD Region
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Search by Peak or Region Search by Peak or Region Midpoint?Midpoint?
Region Peak6790 Genes5270 Genes
1635 Genes115 Genes
5155 Genes
∑ = 6905 Genes
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ContributionsContributions
Cistematic Past Python Code UCSC Genome Broswer
Find Genes within 20Kbp of Potential MyoD
Sites on the genome
See if Expression Level of Genes
ChIP Seq
RNA Seq
Tools
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FindingsFindingsA
vera
ge
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Future DirectionsFuture Directions
Look at correlations of MyoD sites to distances to Look at correlations of MyoD sites to distances to genesgenes Potential regulation distancesPotential regulation distances
CloseClose FarFar BidirectionalBidirectional
Isolated top hits for further analysis:Isolated top hits for further analysis: HighHigh MidMid LowLow
Closer look at MyoD sites with no neighborhood gene Closer look at MyoD sites with no neighborhood gene Reusable analysis for other proteinsReusable analysis for other proteins
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AcknowledgementsAcknowledgements MentorMentor
Barbara WoldBarbara Wold Wold LabWold Lab Biological InvestigatorsBiological Investigators
Brian Williams Brian Williams Ali MortazaviAli Mortazavi
SoCalBSI Faculty and staff SoCalBSI Faculty and staff Jamil MomandJamil Momand Sandy SharpSandy Sharp Nancy Warter-PerezNancy Warter-Perez Wendie JohnstonWendie Johnston
Funding by:Funding by: DOE and NASADOE and NASA NSF, NIH, and NSF, NIH, and
Economic & Workforce Economic & Workforce DevelopmentDevelopment
Computational GurusComputational Gurus Diane TroutDiane Trout Brandon KingBrandon King Cory TobinCory Tobin
Fellow ColleaguesFellow Colleagues Qing YuanQing Yuan Herbert LeeHerbert Lee