1. MCB 317 Genetics and Genomics Topic 11, pt 3 Genomics

2. Genomics Summary A.Microarrays: expression profiling and other uses B.Global Gene Knockouts C.Global protein localization in yeast D.Global complex identification in yeast E.Global two-hybrid analysis in yeast and other organisms F.RNAi G.Transgenics, gene “knock-outs” (genetics not genomics) H.Next Generation Sequencing Genome sequencing ChIP seq RNA seq I.Comparative Genomics, Evolution and Human History

3. Ab Protein Txn Profile Gene Orthologs and Paralogs Mutant Gene Biochemistry Genetics Mutant Organism A C F Subunits of Protein Complex B, G D E Protein Profile/ Localization Genomics: High-throughput genetics Genomics B, G H Gene/Protein DNA binding sites I

4. RNA Seq mRNA or total RNA DNA Sequence “Transcriptome”

5. ChIP Seq DNA pulled down by ChIP Sequence All chromosomal sites bound by YFP

6. Genomics Summary A.Microarrays: expression profiling, RNA seq B.Global Gene Knockouts C.Global protein localization in yeast D.Global complex identification in yeast E.Global two-hybrid analysis in yeast and other organisms F.RNAi G.Transgenics, gene “knock-outs” (genetics not genomics) H.Human Genome Project, Next Generation Sequencing, and Comparative Genomics I.ChIP for specific binding site, ChIP seq for all binding sites throughout the genome

7. Science 296: 1661-1671 Human-Mouse comparison

8. Alb 4-18 MouseHuman Genomic Synteny Map

9. Mouse Chr. 16- Human Comparison Science 296: 1661-1671 31 May 2002 Synteny

10. Human-Mouse Synteny Mouse chr. 16 =Human chr. 3, 8, 12, 16, 21, 22 Mouse chr.16 - Human Gene comparison –731 predicted genes –509 = Orthologs of human in syntenic regions –44 = paralogs –164 = Homologs elsewhere in human genome –14 = No human counterpart (2% unique genes) Look at Human regions of synteny –2.9% genes unique to humans

11. Thinking about Human-Mouse Synteny 85,000,000 years of divergence 300 “flips” 85,000,000/300 = 283,333 years per flip

12. Human-Puffer Fish Synteny 400 million years of divergence Syntenic blocks = 10 Kb in size

13. Generation of Protein Diversity by Alternate Splicing Neurexins are (one type of) neuronal adhesion proteins. They mediate connections between neurons 3 Neurexin Genes -> 2,000 splice variants Human Brain 100 x 10 9 Neurons Each Neuron makes ~1,000 connections Total # of Connections = 100 x 10 12

14. Alternate Splicing and Domain Architecture

16. Major Forces in Evolution of Higher Organisms Gene duplication and divergence -> gene families Alternate Splicing and Domain Architecture Chemical modification ala “histone code” -> lots of chemical modifications to lots of proteins, not limited to histones Not a huge increase in number of genes in humans but each gene -> variety of related proteins

17. Human Evolution from Primates

18. Darwin and Wallace Gave us Natural Selection (Speciation); Mendel gave us a “Mechanism” Species 1 Sp2Sp3 Mutation(s) and Natural Selection

19. Darwin and Wallace: One Species Gives Rise to Another Species 1 Sp2Sp3 Sp4Sp5Sp6Sp7Sp8 Sp9 Sp14 Sp4 Sp10 Sp11Sp12 Sp13 Sp7 Sp16 Sp17 Sp12Sp13 Darwin also realized the reverse was true…

20. Darwin Invented Genealogy! Darwin’s Doctrine of Common Descent: “(P)robably all of the organic beings which have ever lived on this earth have descended from some one primordial form…” Darwin predicted a “…time when we shall have very fairly true genealogical trees of each great kingdom of nature.” Typical Textbook: “All organisms on earth today are the descendants of a single kind of unicellular organism that lived almost 4 billion years ago.”

21. Estimate Time from Common Ancestor Sp14 Sp4Sp11Sp12 Sp13 Sp7 Sp16 Sp17 Time = Mutations/(Mutation Rate)

22. Phylogenetic Tree

23. Human-Chimp Divergence ~ 5,500,000 years ago

24. Within a Population (e.g. Humans) Ind1 Ind2Ind3Ind4 Ind5 Ind6 Ind 7 Ind8 Time = Mutations/(Mutation Rate)

25. Within a Population (e.g. Humans) Ind1 Ind2Ind3Ind4 Ind5 Ind6 Ind 7 Ind8 Look at Mitochondrial Sequences: Maternal Lineage

26. Mitochondrial Eve lived 100,000 - 200,000 years ago 10,000-50,000 human population

27. Look at Y-chromosome: Paternal Lineage Ind1 Ind2Ind3Ind4 Ind5 Ind6 Ind 7 Ind8 Y-chromosome Adam = 95,000 years ago in Sub-saharan Africa ~2,000 men left Africa 67,000 years ago

28. Hartl6 16.5

29. 5,500,000 years ago = divergence of our ancestors from Chimpanzees 600,000 years ago Hominids in Africa 200,000- 300,000 + years ago groups of hominids began leaving Africa and founded populations elsewhere (e.g. Neandertals) 200,000 years ago ~ Homo sapien morphology (look like us) 100,000+ years ago “mitochondiral Eve” was part of a founder population of 10,000 - 50,000 people 95,000 years ago -> Y-chromosome “Adam” lived in Sub-saharan Africa 30,000-50,000 years ago the population of humans that left Africa inter- bred with Neanderthals in the Middle East -> People of European and Asian descent have some Neanderthal alleles -> skin phenotypes: skin color and keratin intermediate filaments Model from a Collection of Recent Data

30. Evolution of Keratins Keratin family seems to have arisen at the time that animals with soft exteriors appeared. Animals that lack an exoskeleton.

31. Roles of Intermediate Filaments Distribute tensile forces across cells in tissues Integrate cells into tissues

32. Intermediate Filaments and Human History

33. Neanderthal-Human divergence ~600,000 years ago Modern Humans migrated out of Africa ~100,000 years ago Humans interbred with Neanderthals ~50,000-60,000 years ago in Middle East Modern Humans migrated to Europe and Northern Asia ~40,000-45,000 years ago Neanderthals died out ~30,000 years ago

34. Sequencing Neanderthal Genomes and Comparing DNA with Modern Humans The complete genome sequence of a Neanderthal from the Altai Mountains Nature 2 Jan 2014; 505:43 Resurrecting Surviving Neandertal Lineages from Modern Human Genomes Science 28 February 2014; 343:1017

35. Human DNA Derived from Neanderthals in non-Africans 1.BNC2 a zinc finger protein associated with skin pigmentation 2.POUF2F3 a transcription factor expressed in epidermis that mediates keratinocyte proliferation and development 3.A cluster of keratin genes

36. Common Chimps (Pan troglodytes), Bonobos (Pan paniscus, or pygmy chimps), the Congo River and 1-2 million years of evolution… …and 6.5 million years of evolutionary divergence from Homo sapiens: comparative genomics of primates

37. Svante Paabo: Human FOXP2 allele ~200,000 to 50,000 yrs ago -> speech and language. Could the development of advanced speech and language be the result of the human FOXP2 allele? The human WT allele differs in 2 positions from the WT chimp allele. Originally speculated to have occurred after our split from Neanderthals; however, recent data indicates that the FOX2P language allele that humans have but that chimps lack was also found in Neanderthal DNA FOX2P was subject to a “genetic sweep”

38. Micro-encephalin contributes to brain size Human allele arose ~ 37,000 years ago which corresponds to the time that art, music and advanced tool-making emerged in the human population; however note that the date of 37,000 years ago comes with error bars of 23,000 years [but how does this fit with the idea that Y Adam and Mito Eve existed 100,000 years ago?

39. ASPM a gene also involved in brain size/development. Human specific allele is thought to have arisen only 5,800 years ago. Newspaper version: “This is approximately time time when language, agriculture and cities began to appear.” Gene v. allele Correlation v. actual evidence 5,800 yrs, v. 500 -14,000 yrs Statements/observations like this are in the early stages of understanding and are controversial… if not down-right wrong! Human Specific ASPM Allele

40. Comments on Genetic Diversity and Evolution

42. 35 Generations

43. Mitochondrial Eve and Y-chromosome Adam ~ 100,000 years ago Assume 15 yrs/generation 100,000/15 = ~ 6,700 generations of modern Homo sapiens If 20 yrs/generation 100,000/20 = ~ 5,000 generations of modern Homo sapiens

44. Comments on Life on Our Planet

47. Timeline of the Universe and Earth 0Time (Billions of Years) 14.510 20 Estimated Lifespan of our Sun What type of atoms were created in the big bang?

48. Timeline of the Universe and Earth 0Time (Billions of Years) 14.510 20 Estimated Lifespan of our Sun Massive stars created the “heavy” elements ( > H) and exploded spreading those elements, which formed new stars and planets…. including us…

49. The Birth of “Our” “Heavy” Atoms

50. Some Major Events in Evolution and Biological History From birth of heavy atoms To formation of molecular O 2 To mitochondria and nuclei To dinosaurs Ice age -> humans…. Human chimp divergence