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

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

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

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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)

Are the Close Genes Are the Close Genes Expressed?Expressed?

Genomic DNA

Nearby GenesNearby Genes

Solexa

RNA Sequencing (RNASeq)RNA Sequencing (RNASeq)

Introns ExonsExons

AAAAA Pre-mRNAAAAAA mRNA5’ cap

Reverse Transcription

DNA

Solexa/Illumina

Size Selected

DNA

TranscriptionProcessing…

How are Genes Expressed?How are Genes Expressed?

Genomic DNA

Introns ExonsExons

Solexa/Illumina

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

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Location of RegulatorsLocation of Regulators

Gene A Gene BGene CDNASite

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

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

Hits at Hits at PeaksPeaks and in and in RegionsRegions

MyoD Region

Search by Peak or Region Search by Peak or Region Midpoint?Midpoint?

Region Peak6790 Genes5270 Genes

1635 Genes115 Genes

5155 Genes

∑ = 6905 Genes

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

FindingsFindingsA

vera

ge

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

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