HC70A & SAS70A Winter 2011 Genetic Engineering in Medicine, Agriculture, and Law Professors Bob Goldberg & John Harada Lectures 5 & 6 The Age of Genomics:Your Personal Genome & Tracing Your Ancestry Course AdministratorpTHEMES 1. Two Genomes in a Cell! 2. What is the Mitochondrial Genome and How is it Inherited? 3. What Are the Characteristics of the Human Genome? 4. The Age of the Personal Genome Has Arrived! 5. How Many Mammalian Genomes Have Been Sequenced and What Can We Learn From Comparative Genomics? 6. How Does Genetic Variation Arise in the Human Genome? 7. How to Use DNA Markers to Find Human Disease Gene Alleles? 8. How to Detect DNA Sequence Variation: SNPs and VNTRs? 9. What Can SNPs Be Used For? 10. Tracing Human Ancestry Using SNPs 11. Are Their Human Races? 12. Knowledge or Certainty?Human Cells Have Two Genomes………One in the Nucleus and One in the Mitochondria Do Nuclear & Mitochondrial Genes Have Different Inheritance Patterns?The Nuclear and Mitochondrial Genomes in Size & Shape Nuclear Mitochondrial 3.2 Mb 25,000 Genes 24 Linear Pieces 17 kb 30 Genes 1 CircleThe Nucleus Is A Complex Organelle With 23 Pairs of Chromosomes (Humans) Packing Problem? The Human Genome End to End is 1.1 Meters in Length!!!!!! Note: Chromosome Sizes & Bands = Markers RNA & Protein TransportThe Human Karyotype Note: Chromosome Sizes & Bands = Markers 3.2 x 109 bp (3.2 Mb)The Mitochondrial GenomeSemi-Autonomous Genome DNA Divides Transcription Translation Mitochondrial Proteins Mitochondria Power Human Cells and Contain a Circular Genome Makes ATP Energy That Powers All Cells!Mitochondrial DNA Diseases Affect 1/400 PeopleMERRF: A Mitochondrial Disease Example No Mitochondria In Sperm Heads EggMitochondrial Genes Are Inherited: a. Paternally b. MaternallyThe Circular Mitochondrial Genome is Inherited Maternally Disease Genes Present on the Mitochondrial Genome Many Affect Muscles Because Mitochondria Produce Energy Needed For Muscle ActivityHow Are Mitochondrial Gene Defects Inherited? No Mitochondria In Sperm Heads Egg Note Maternal Inheritance: Disease Passed From Mother to All of Her Children and Not Passed on By FatherNature 461, September 17, 2009 Mito and TrackerFuture Mitochondrial Gene Replacement Therapy Normal Mitochondria Mutant Mitochondria Note: The Zygote Contains THREE Genomes -- One from Mother, One From Father, and One From Donor Mitochondria 1 2 3• How to Test Whether It Works? • Testing on Live Human Embryos • When To Test Its Effectiveness • Safety & Long-Term Potential Problems • Research Protocols & Oversight • Informed Consent of Parents British Medical Journal, January 8, 2011,342, 87-89RFLPs Can Be Used to Identify Individuals Using Mitochondrial DNAs Note How Mitochondrial RFLP Markers Are Inherited !! 100% of Children Have 8.6 kb DNA Fragment From MotherTracing Human Populations Using Mitochondrial DNA Polymorphisms - Back to Eve!Oldest Populations Contain the Most Diversity Oldest Population Newest Population Time Lots of “Old” Variants Subset of “Old” Variants + New Variants Detected By Using Specific Markers (RFLPs or SNPS) Old Variants Trace Ancient Lineage. New Variants Mark New Populations SPECIFICALLYMost Genetic Diversity Originated in the Founder Populations to Modern Humans! 1. Most Variation 2. Migration of Subset of Population 3. Subset of Original Variability + New Mutations/Variability Genetic Variation Proportional to Population Age Younger Populations Less Genetic Variability Markers From Original Population + New Markers For “New” PopulationThe Nuclear Genome Note: Gene is Inherited in a Mendelian Pattern Dominant or Recessive?The Human Genome Was Sequenced Ten Years Ago! The Human Genome Project Public & Private Effort Using Different Strategies - A Race! 3 Billion Dollars & Took 15 YearsToday-We Can Sequence an Individual’s Genome in Two Hours For ~$700!!!!! The Public Human Genome Project Cost 3 Billion Dollars & Took 15 YearsThe Human Genome Could Not Have Been Sequenced Without The Invention of Genetic Engineering Genes Need to Be Cloned Before They Can Be Sequenced!!!!!!! The Age of Genomics is a Result of the Age of Genetic Engineering Cohen & Boyer Experiment That “Invented” Genetic EngineeringThe Human GenomeOnly A Small Fraction of the Human Genome Encodes Proteins Human Genes are Large but Contain Mostly Introns The Human Genome Has DNA Sequences Present Once As Well as Repeated Many TimesTable 4-1 Molecular Biology of the Cell (© Garland Science 2008) Characteristics of the Human Genome Duchenne Muscular Dystophy Smallest Gene is 252 bp & Ecodes an Insulin-like Growth factorThe Human Genome Contains ~25,000 Different Genes How Many Encoded Proteins? Alternative Splicing? Do Not Know Functions of Most Human Genes! Use Bioinformatics To Identify Gene FunctionsAlternative Splicing- One Gene Several mRNAs & Proteins Implication- Human Genome Has Only 25,000 Genes But Can Give Rise to Many More Proteins which Are Responsible For Producing the Phenotype Reason Why Human Genome Can Contain Same Number of Genes as Fly and Plant Genomes!! Implications for Genetic Engineering? Use Specific cDNA! Gene Activity in Varity of Cells, But…..!!! 5 Different mRNAs! Different mRNA = Different Proteins = Different Functions!How Many Human Disease Genes Have Been Identified? There are ~25,000 Genes in The Human Genome 1. ~2,700 Genes Correlate With a Disease Phenotype 2. The Molecular Basis of 90% of These Genetic Diseases Are Known (e.g., Sickle Cell Anemia, Hemophilia A) Nature Education!1(1),!(2008) http://www.nature.com/scitableExamples of Human Disease Genes That Are Known Genetic Tests Exist For These Disease GenesThe Human Genome Landscape Tandem Repeats or VNTRs are Useful for DNA Fingerprinting Studies! e.g., DIS80 Locus For Class DNA Fingerprint on Chromosome 4 Core = 16bp Tandem Repeats (VNTR) Transposons Mendelian Gene 1 2DNA Sequencing Throughput Has Exploded!Cost of Sequencing is Going Down Precipitously!1. Clone DNA Fragments and/or Genome 2. Sequence One DNA Fragment at a Time Sequencing the “Old Fashioned” Way • 500 bp/lane • Radioactivity • Autoradiograms • 24 Hrs • Manual • Chemicals Maxam & Gilbert, 1975New Sequencing Technologies Have Lead To An Explosion of Whole Genome Sequencing http://www.genomesonline.org/cgi-bin/GOLD/bin/gold.cgi 9640