DISCOVERING GENOMICS, PROTEOMICS, AND BIOINFORMATICS

DISCOVERING GENOMICS, PROTEOMICS, AND BIOINFORMATICS Second Edition A. Malcolm Campbell Laurie J. Heyer

Foreword ix New Paradigms : Nonstructural Causes for Muscula r Preface xi Dystrophies 23 Acknowledgments xiv Final Presentation 2 7 Math Minute 1.4 Is cgmp Production Elevated? 2 8 SUMMARY 1.2 29 Unit One Chapter 1 Conclusions 29 References 2 9 Genome Sequences 1 CHAPTER 1 CHAPTER 2 What's Wrong with My Child? 2 Genome Sequence Acquisition 33 2.1 How Are Genomes Sequenced? 34 1.1 First Patients 3 What Is Genomics? 3 4 Phase I: Clinical Presentation 3 Phase II: Family Pedigree 4 How Are Whole Genomes Sequenced? 34 Phase III : Karyotyping and Linkage Analysis 5 How Are Organisms Picked for Genome Sequencing? 3 6 Phase IV: DNA Sequence Analysis 5 SUMMARY 1.1 7 Math Minute 1.1 What Is an E-Value? 7 1.2 The Next Steps in Understanding the Disease 9 The Need for an Animal Model System 9 What Was the Other Protein that Gave Lots of BLASTp Hits? 9 Does Utrophin Play a Role in Muscular Dystrophy, Too? 10 What Does Dystrophin Do? 10 Math Minute 1.2 What's Special about This Graph? 12 Why Do DMD Patients' Muscles Deteriorate after the First Three Years? 13 Is It Possible to Have DMD and Be Wild-Type for Dystrophin? 13 How Can They Have Muscular Dystrophy if Their Dystrophin Genes Are Normal? 14 Math Minute 2.1 What Can You Learn from a Do t Plot? 4 0 Math Minute 2.2 How Do You Find Motifs? 4 2 Can We Predict Protein Functions from DN A Sequence? 4 5 Math Minute 2.3 What Are "Positives" and What Do They Have to Do with E-values? 4 6 What Shapes Are the Proteins? 4 8 Does Structure Reveal Function? 49 Why Do the Databases Contain So Many Partia l Sequences? 4 9 Which Sequencing Method Worked Better? 5 1 Annotated Genomes Online 5 4 How Many Proteins Can One Gene Make? 54 Can the Genome Alter Gene Expression Without Changing the DNA Sequence? 5 5 What Is the Fifth Base in DNA? Methyl-Cytosine 5 7 Imprinting, Methylation, and Cancer 5 8 Math Minute 1.3 What Do You Mean by Highly Unlikely? 15 SUMMARY 2.1 59 Where Is the Muscular Dystrophy Field Now? 20 Sixth International Conference on Molecular Causes 2.2 What Have We Learned from Unicellula r of Muscular Dystrophies 20 Genomes? 5 9 The Meeting Begins 20 Why Do I Get So Many Pimples? 5 9 Structural Weaknesses 20 Which Genes Cause Pimples? 60 Nonfunctional Mutations 22 Are All Bacteria Living in Us Bad for Us? 62

Can Microbial Genomes Become Dependent upon CHAPTER 3 Human Genes? 64 Comparative Genomics in Evolution and Medicine 11 3 What Is the Minimum Number of Genes Possible? 6 5 Are All Viral Genomes Smaller than All Bacterial 3.1 Comparative Genomics 11 4 Genomes? 66 How Can E. tali Be Lethal and in Our Intestines at the Same Time? 114 Is Mimivirus Alive? 67 Do Genomes Reflect an Organism's Ecological Niche? 68 Math Minute 2.4 Can You Estimate the Number of Inversion s in a Dot Plot? 70 Why Is MED4's Genome So Small? 72 Math Minute 3.1 How Can You Tell if Base Compositions Are Different? 11 5 Two Hundred Genomes : What Can Comparative Genomics Tell Us about Prokaryotes? 11 6 Do All Prokaryotes Have One Circular Chromosome? 11 6 How Many Genome Changes Are Required Before a New Are the Genomes Still Changing? 11 7 Species Is Created? 73 How Many Genomes Are There? 11 8 What Kind of Organism Causes Malaria? 74 What Can We Learn by Comparing Many Whol e What Sort of Genome Does Plasmodium Possess? 75 Genomes? 12 1 Is the Predicted Proteome Equally Bizarre? 76 What Can We See at the Chromosomal Perspective? 12 3 Is There a Model Eukaryore Genome? 78 SUMMARY 3.1 14 What Did the Investigators Predict for the Future o 5 f Genomics? 81 3.2 Evolution of Genomes 12 6 Epilog for the Yeast Genome 81 What Organism Is the Root of the Tree of Life? 12 6 SUMMARY 2.2 83 What Are the Origins of our Nuclear Genes? 12 9 2.3 What Have We Learned from Metazoan Math Minute 3.2 Are the Hit Numbers Significantly Different 13 2 Genomes? 83 Is There Evidence of Intermediate Stages in Genomi c Are Animal Genomes Harder to Finish? 83 Evolution? 132 What Are Polythene Chromosomes? 83 Are You Going to Eat That? 13 3 A Missing Link of Biblical Proportions 136 What Makes a Fly Different from Other Eukaryotes? 8 7 Could Nuclei Evolve without Symbiosis? 137 Is the Fly Still a Good Model Organism? 88 Are We Related to Rats? 13 8 Fly Genome Epilog 89 What Is the Origin of Our Species? 13 9 Do We Need Two Plant Genome Sequences? 90 Are We All of African Descent? 14 1 Plants Seem Simpler than Animals, but Are Their Genomes? 91 Math Minute 3.3 How Do You Know if the Tree Is Correct? 143 Can We Draw Any Conclusions from Draft Sequences? 91 Have We Stopped Evolving? 14 3 What Lessons Have We Learned? 94 SUMMARY 3.2 14 5 Rice Epilog 9 5 3.3 Genomic Identifications 14 5 What Can We Possibly Learn from a Puffer Fish Genome? 96 How Can We Identify Biological Weapons? 14 5 Did the Genome Reveal Any Surprises? 97 How Long Can DNA Survive? 14 9 Are There More Big Lessons from Tetraodon? 98 How Did Tuberculosis Reach North America? 15 2 What Makes Humans Different? 99 How Are Newly Emerging Diseases Identified? 15 5 What Other Outbreaks Are Coming? 15 9 Math Minute 2.5 How Do You Fit a Line to Data? 101 SUMMARY 3.3 16 1 Whose DNA Did We Sequence? 102 3.4 Biomedical Genome Research 16 2 Can We Describe a Typical Human Gene? 103 Can We Use Genomic Sequences to Make New Human Genome Epilog 106 Vaccines? 162 What Is the Next Goal in Human Genomics? 108 Can We Make New Types of Antibiotics? 16 4 SUMMARY 2.3 109 Can We Invent a New Class of Medication? 166 Chapter 2 Conclusions 109 Is There an Alternative Way to Inhibit RNAs? 16 9 References 109 Are There More Stable RNA Genomes We Can Target? 170

SUMMARY 3.4 172 Unit Tw o Chapter 3 Conclusions 172 Genome Expression 21 7 References 172 CHAPTER 4 CHAPTER 5 Genomic Variations 177 Why Can 't I Just Take a Pill to Lose Weight? 21 8 4.1 Environmental Case Study 178 Hungry for Knowledge 21 9 Can Genomic Diversity Affect Global Warming? 178 Saturday, 21 October. 7:30 A.M. 21 9 Math Minute 4.1 How Do You Measure Genetic Library Opens at 8:30 A.M. on Saturdays 21 9 Diversity? 180 Building a Model for Weight Homeostasis 220 Cloning the Leptin Gene 22 0 Math Minute 4.2 How Do You Model Populatio n Diversity? 184 Functional Tests for Leptin 22 3 SUMMARY 4.1 186 Time to Visit Grandma 224 Grandma Gives You Homework! 22 4 4.2 Human Genomic Variation 186 Chapter 5 Conclusions How Much Variation Is in the Human Genome? 186 References 23 1 23 1 What 's the Difference Between a Mutation and an Allele? 187 Why Should We Care about NSPs? 188 Math Minute 4.3 Are All SNPs Really SNPs? 188 Do Any SNPs Produce Common Phenotypes? 19 2 Are There Vital SNPs That Can Surprise Me? 194 Patent Law and Genomics 195 CHAPTER 6 Basic Research with DNA Microarrays 23 3 6.1 Introduction to Microarrays 23 4 What Happened to My Home Brew? 234 Where's the Probe? 23 5 Why the SNP Frenzy? Pharmacogenomics! 196 Microarray Data Look Good, but Are They Real? 237 SUMMARY 4.2 198 How Do You Analyze These Data? 23 8 4.3 The Ultimate Genomic Phenotype-Death? 198 Math Minute 6.1 Why Should You Log-Transform Microarra y Why Do We Age? 199 Data? 23 9 Are There Hidden Costs for a Prolonged Life? 200 Math Minute 6.2 How Do You Measure Similarity betwee n Do Bacteria Experience Genomic Tradeoffs Too? 201 Expression Patterns? 24 0 SUMMARY 4.3 202 4.4 Ethical Consequences of Genomic Variations 203 Are Genetically Modified Organisms Bad? 203 Is Genetic Testing Good? 205 Math Minute 4.4 What Does a Positive Test Result Really Mean? 208 Math Minute 6.3 How Do You Cluster Genes? 24 1 Can Chips Reveal Regulatory Sequences? 24 5 Can We Formulate Testable Predictions with Thes e Data? 24 5 Microarrays Seem Too Good to Be True-Are They? 248 Why Did the Beer Blow? 249 What Can We Learn from Stressed-Out Yeast? 250 Do Fungi Feel Stress? 25 1 Genomic Diversity Banks and Small Populations 209 What Goes Up? 25 1 Who Benefits from Genomic Medicine? 210 Why Are There So Many Copies of Some Genes but No t Are There Simple Applications for Complex Others? 25 2 Genomes? 210 How Well Do Promoters Control Gene Expression? 25 3 Should I Get a Genetic Test? 211 Do Promoters Work in Reverse? 254 Should Humans Be Cloned? 212 SUMMARY 6.1 25 4 SUMMARY 4.4 214 6.2 Alternative Uses of DNA Microarrays 25 4 Chapter 4 Conclusions 214 Why Do So Many Unrelated Genes Share the Sam e References 214 Expression Profile? 255

Math Minute 6.4 Is It Useful to Compare the Columns of a Gene Can We Use Structures to Develop Better Drugs? 297 Expression Matrix? 256 Can One Protein Kill You? 29 7 Can Cells Verify Their Own Genes? 258 SUMMARY 8.2 299 Which Predicted Genes Are Real and Which Ones 8.3 Protein Interaction Networks 29 9 Aren't? 259 Which Proteins Interact with Each Other? 29 9 Can Microarrays Improve Annotations? 259 Can Sequence Analysis Uncover Interactions? 30 0 Could a Microarray Validate Annotation of an Entire Can We Detect Protein Interactions? 30 0 Genome? 259 Math Minute 8.2 Is Sup35 a Central Protein in the Network? 30 3 SUMMARY 6.2 261 Is It Possible to Understand Proteome-Wid e Chapter 6 Conclusions 261 Interactions? 30 4 References 261 SUMMARY 8.3 30 6 CHAPTER 7 8.4 Measuring Proteins 30 7 Which Proteins Are Present? 307 Applied Research with DNA Microarrays 263 What Are 2D Gels? 30 7 7.1 Cancer and Genomic Microarrays 264 What Proteins Do Our White Blood Cells Need to Kill a Are There Better Ways to Diagnose Cancer? 264 Pathogen? 31 0 Math Minute 7.1 What Are Signature Genes, and How DoYour Minute 8.3 How Do You Identify Proteins on 2D Gels? 31 1 Use Them? 266 How Much of Each Protein Is Present? 314 Can Breast Cancer Be Categorized with Microarrays? Can We Quantify Proteomes in Cultured Cells? 31 4 268 Can We Quantify Proteins in Any Cell? 31 6 What Genomic Changes Occur in Cancer Cells? 270 Nice Idea, But Does ICAT Work? 31 6 Is the Last Unexplored Ecosystem on Earth Inside th e SUMMARY 7.1 272 Cell? 319 7.2 Improving Health Care with DNA Can We Make Protein Microarrays? 32 0 Microarrays 273 Can Microarrays Detect Proteome Interactions? 32 0 Why Is the Tuberculosis Vaccine Less Effective Now? 273 Can Protein Microarrays Measure Kinase Activity? 32 1 Can We Choose the Most Effective Medication for Each Are All Cells Equal? 323 Cancer? 276 Can We Predict Effectiveness of Chemotherapy? 27 6 What Happens When You Accumulate Fat? 277 What Does a Proteome Produce? 32 5 SUMMARY 8.4 32 7 What Effect Does Leptin Have on wt Adipose Tissue? 281 Chapter 8 Conclusions 327 References 327 SUMMARY 7.2 28 2 Chapter 7 Conclusions 282 Unit Three References 282 Whole Genome Perspective 329 CHAPTER 8 CHAPTER 9 Proteomics 285 Why Can't We Cure More Diseases? 33 0 8.1 Introduction 285 What Do All These Proteins Do? 286 Where Are These Proteins Located? 289 Which Proteins Are Needed in Different Conditions? 290 Math Minute 8.1 How Do You Know if You Have Sampled Enough Cells? 292 SUMMARY 8.1 294 How Are New Medications Developed? 33 1 Focus 1 : Location, Location, Location 33 1 Focus 2: Delivery Vehicles 33 1 Focus 3 : Specificity 333 Math Minute 9.1 What's the Right Dose? 33 5 How Many Drugs Does It Take to Cure a Disease? 33 6 What Type of Drug Works Best? 336 8.2 Protein 3D Structures 295 Can Medication Do More than Simply Mas k Does a Protein's Shape Reveal Its Function? 295 Symptoms? 337

Do We Know the Answers? 338 What Effect Do Noise and Stochastic Behavior Hav e Chapter 9 Conclusions 339 on a Cell? 37 1 References 340 Math Minute 11.1 How Are Stochastic Models Applied to Cellular Processes? 37 1 CHAPTER 10 Theory Is Nice, but Do Toggle Switches Reall y Exist? 374 Genomic Circuits in Single Genes 341 How Can Multicellular Organisms Develop with Noisy Circuits? 37 6 10.1 Dissecting a Gene's Circuitry 342 Redundancy : Does Gene Duplication Really Increase How Are Genes Regulated? 342 Genome Reliability? 37 7 Molecular Dissection of Development 343 Does Memory Formation Require Toggle Switches? 37 8 Expression ofendo16 343 Are Simple Models of Complex Circuit s How Does a Gene Control Location, Timing, and Worthwhile? 380 Quantity of Transcription? 344 How Much Math Is Required to Model Memory? 38 0 Which Modules Control Location? 344 How Do You Build Complex Models? 38 1 Why Do Modules F, E, and DC Promote Expression in Can a Transient Stimulus Produce Persistent Kinase the Wrong Cells? 345 Activation? 38 1 How Does Lithium Affect Transcription? 348 Why Does 100 Minutes of 5 nm EGF Achiev e What Controls the Timing of Endol6Transcription? 350 Long-Term Activation? 38 2 Does Module G Have a Function? 351 Math Minute 11.2 Is It Possible to Predict Steady-Stat e Can We Draw a Transcription Circuit for Endol6? 352 Behavior? 384 What Makes Module A So Special? 355 Can the Modeled Circuit Accommodate Learnin g How Do Module A-Binding Proteins Work? 355 and Forgetting? 38 5 Which Module A Sites Respond to Repression by Modules What Roles Do Other Integrated Circuits Play DC, E, and F? 359 in LTP? 38 6 How Does Module A Interact with the Basic Do They Need a More Complex Model to Matc h Promoter? 360 Reality? 38 7 Are Genes Hard-Wired? 361 Are LTP and Long-Term Memory Related? 39 0 Do Genes Contain Miniature Computer Programs? 363 What Have We Learned (How Much LTP Have We Math Minute 10.1 How Do You Make a Computer Understand Generated)? 39 1 Gene Regulation? 364 Can We Understand Cancer Better by Visualizing Its Circuitry? 39 1 SUMMARY 10.1 366 10.2 Integrating Single-Gene Circuits 36 6 SUMMARY 11.1 39 3 How Can We Describe to Others What We Know About 11.2 Synthetic Biology 39 4 a Genome Circuit? 366 Can Humans Engineer a Genetic Toggle Switch? 39 4 Does Interactivity Enhance Understanding? 366 How to Build a Toggle Switch 394 Technical Hints 366 Can We Build a Synthetic Oscillating Clock? 39 6 SUMMARY 10.2 367 Math Minute 11.3 How Can You Visualize Gene Regulatio n Logic? 39 7 Chapter 10 Conclusions 367 References 368 Can Synthetic Devices Alter Gene Expression? 40 0 If Circuits Are Interconnected, Does Gene Orde r Matter? 40 2 CHAPTER 11 Observational Approach 40 2 Integrated Genomic Circuits 369 Computational Approach 40 3 11.1 Natural Gene Circuits 370 Does Gene] Have to Be First? 40 4 Can Genes Form Toggle Switches and Make SUMMARY 11.2 40 7 Choices? 370 Chapter 11 Conclusions 407 How Do Toggle Switches Work? 370 References 407

CHAPTER 12 Modeling Whole-Genome Circuits 409 Context of the Message: What Is the Impact of thi s Research? 41 7 12.1 Is Genomics a New Perspective? 410 12.3 Will Systems Biology Go Systemic? 41 8 The People Involved : Who Is Doing Systems Chapter 12 Condusions 41 9 Biology? 410 References 419 The Quality of the Message : What Questions Do Systems Biologists Ask? 41 1 Glossary 42 1 12.2 Can We Model Entire Enkaryotes with a Systems Approach? 411 Credits 435 Does the Proteome Respond Like the Transcriptome? 415 Index 439 Can We Build a Systems Model? 416