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Target Gene Predictions for MyoD Genome-Wide Dr. Barbara Wold’s Lab (Caltech)

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

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Target Gene Predictions for MyoD Genome-Wide Dr. Barbara Wold’s Lab (Caltech)

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  1. Target Gene Predictions for MyoD Genome-Wide Dr. Barbara Wold’s Lab (Caltech) Sean Caonguyen SoCalBSI 8/15/2007

  2. Outline • Background • Regulation of Muscle Development • Chromatin Immunoprecipitation Sequencing (ChIPSeq) • RNA Sequencing (RNASeq) • Biological Significance • Approach • Cistematic Python Package • UCSC Genome Browser • Findings • Distance from MyoD Regions and Peaks to closest Gene • Compare close genes to the expressed genes • Future Directions

  3. Early Regulation of Muscle Development • Why are Muscles Important? • For daily activities • To maintain biological composition • TO LIVE!! • Myogenic Regulatory Factors (MRFs) • Myf 5 • MyoD • Myogenin • Mrf 4 http://files.myopera.com/honeybe/blog/wCars002%2520-%2520car%2520cartoon.jpg

  4. CHROMOSOMAL DNA Each red box denotes a sequence read Map sequence to genome Chromatin Immunoprecipitation Sequencing (ChIPSeq) MyoD DNA • Johnson, D.S., et al. (2007) • and Fields, S. (2007)

  5. Are the Close Genes Expressed? Solexa Nearby Genes Genomic DNA

  6. RNA Sequencing (RNASeq) DNA Introns Exons Transcription Processing… 5’ cap AAAAA mRNA AAAAA Pre-mRNA Reverse Transcription DNA Size Selected Solexa/Illumina

  7. How are Genes Expressed? Solexa/Illumina Exons Introns Genomic DNA

  8. Biological Significance of Analysis • Help understand regulation for the muscle network genes • Problems with Muscle Atrophy: • 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

  9. Location of Regulators DNA Gene A Gene B Gene C Site

  10. Approach to Project • Tools • Cistematic Python Package created by Ali Mortazavi • Data and Code from Ali Mortazavi and Qing Yuan • UCSC Genome Browser • Tasks • Look at MyoD enriched regions • Find distance to nearby genes • Determine which genes are expressed or suppressed

  11. Find Neighborhood Genes • Look for genes in 20kbp radius of the MyoD sequence-tag-enriched regions • Also determine distance to the peaks in regions MyoD Region Gene Gene Gene Gene Gene Gene DNA

  12. Hits at Peaks and in Regions MyoD Region

  13. Search by Peak or Region Midpoint? 5155 Genes 115 Genes 1635 Genes Region Peak 5270 Genes 6790 Genes ∑ = 6905 Genes

  14. 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

  15. Findings Average

  16. Future Directions • Look at correlations of MyoD sites to distances to genes • Potential regulation distances • Close • Far • Bidirectional • Isolated top hits for further analysis: • High • Mid • Low • Closer look at MyoD sites with no neighborhood gene • Reusable analysis for other proteins

  17. Mentor Barbara Wold Wold Lab Biological Investigators Brian Williams Ali Mortazavi SoCalBSI Faculty and staff Jamil Momand Sandy Sharp Nancy Warter-Perez Wendie Johnston Funding by: DOE and NASA NSF, NIH, and Economic & Workforce Development Computational Gurus Diane Trout Brandon King Cory Tobin Fellow Colleagues Qing Yuan Herbert Lee Acknowledgements

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