mcb 317 genetics and genomics topic 11, pt 3 genomics
TRANSCRIPT
MCB 317Genetics and Genomics
Topic 11, pt 3Genomics
Genomics Summary
A. Microarrays: expression profiling and other usesB. Global Gene Knockouts C. Global protein localization in yeast D. Global complex identification in yeast E. Global two-hybrid analysis in yeast and other organismsF. RNAiG. Transgenics, gene “knock-outs” (genetics not genomics)H. Next Generation Sequencing
Genome sequencingChIP seqRNA seq
I. Comparative Genomics, Evolution and Human History
Ab
Protein
TxnProfile
Gene
Orthologs and Paralogs
Mutant Gene
Biochemistry
Genetics
Mutant Organism
A
C
F
Subunits of Protein Complex
B, G
D E
ProteinProfile/Localization
Genomics:
High-throughput genetics
Genomics
B, G
H
Gene/Protein
DNA binding sites
I
RNA Seq
mRNA or total RNA
DNA
Sequence
“Transcriptome”
ChIP Seq
DNA pulled down by ChIP
Sequence
All chromosomal sites bound by YFP
Genomics Summary
A. Microarrays: expression profiling, RNA seqB. Global Gene Knockouts C. Global protein localization in yeast D. Global complex identification in yeast E. Global two-hybrid analysis in yeast and other organismsF. RNAiG. Transgenics, gene “knock-outs” (genetics not genomics)H. Human Genome Project, Next Generation Sequencing,
and Comparative GenomicsI. ChIP for specific binding site, ChIP seq for all binding
sites throughout the genome
Science 296: 1661-1671
Human-Mouse comparison
Alb 4-18
Mouse Human
Genomic Synteny Map
Mouse Chr. 16- Human
Comparison
Science 296: 1661-167131 May 2002
Synteny
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
Thinking about Human-Mouse Synteny
• 85,000,000 years of divergence• 300 “flips”• 85,000,000/300 = 283,333 years per flip
Human-Puffer Fish Synteny
• 400 million years of divergence• Syntenic blocks = 10 Kb in size
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 109 NeuronsEach Neuron makes ~1,000 connectionsTotal # of Connections = 100 x 1012
Alternate Splicing and Domain Architecture
Alternate Splicing and Domain Architecture
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
Human Evolution from Primates
Darwin and Wallace Gave us Natural Selection (Speciation); Mendel gave us a “Mechanism”
Species 1
Sp2 Sp3Mutation(s) and Natural Selection
Darwin and Wallace: One Species Gives Rise to Another
Species 1
Sp2 Sp3
Sp4 Sp5 Sp6 Sp7 Sp8
Sp9
Sp14 Sp4
Sp10
Sp11 Sp12 Sp13 Sp7 Sp16 Sp17
Sp12 Sp13
Darwin also realized the reverse was true…
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.”
Estimate Time from Common Ancestor
Sp14 Sp4 Sp11 Sp12 Sp13 Sp7 Sp16 Sp17
Time = Mutations/(Mutation Rate)
Phylogenetic Tree
Human-Chimp Divergence ~ 5,500,000 years ago
Within a Population (e.g. Humans)
Ind1 Ind2 Ind3 Ind4 Ind5 Ind6 Ind 7 Ind8
Time = Mutations/(Mutation Rate)
Within a Population (e.g. Humans)
Ind1 Ind2 Ind3 Ind4 Ind5 Ind6 Ind 7 Ind8
Look at Mitochondrial Sequences: Maternal Lineage
Mitochondrial Eve lived 100,000 - 200,000 years ago
10,000-50,000 human population
Look at Y-chromosome: Paternal Lineage
Ind1 Ind2 Ind3 Ind4 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
Hartl6 16.5
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
Evolution of Keratins
Keratin family seems to have arisen at the time that animals with soft exteriors appeared. Animals that lack an exoskeleton.
Roles of Intermediate Filaments
Distribute tensile forces across cells in tissues
Integrate cells into tissues
Intermediate Filaments and Human History
Intermediate Filaments and Human History
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
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
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
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
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”
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?
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. alleleCorrelation v. actual evidence5,800 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
Comments on Genetic Diversity and Evolution
35 Generations
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
Comments on Life on Our Planet
Timeline of the Universe and Earth
0 Time(Billions of Years)
14.510
10 20
Estimated Lifespanof our Sun
What type of atoms were created in the big bang?
Timeline of the Universe and Earth
0 Time(Billions of Years)
14.510
10 20
Estimated Lifespanof our Sun
Massive stars created the “heavy” elements ( > H) and exploded spreading those elements, which formed new stars and planets…. including us…
The Birth of “Our” “Heavy” Atoms
Some Major Events in Evolution and Biological History
From birth of heavy atoms
To formation of molecular O2
To mitochondria and nuclei
To dinosaurs
Ice age -> humans….
Human chimp divergence