Transcript genetics not genomics

MCB 317
Genetics and Genomics
Topic 11, pt 3
Genomics
Genomics Summary
A.
B.
C.
D.
E.
F.
G.
H.
I.
Microarrays: expression profiling and other uses
Global Gene Knockouts
Global protein localization in yeast
Global complex identification in yeast
Global two-hybrid analysis in yeast and other organisms
RNAi
Transgenics, gene “knock-outs” (genetics not genomics)
Next Generation Sequencing
Genome sequencing
ChIP seq
RNA seq
Comparative Genomics, Evolution and Human History
Genomics
Biochemistry
Subunits of Protein
Complex
Genomics:
High-throughput
genetics
Protein
D
Orthologs and
Paralogs
E
H
Gene
Ab
B, G
A
F
Gene/Protein
Txn
Profile
Mutant Gene
B, G
I
DNA binding sites
C
Protein
Profile/
Localization
Mutant Organism
Genetics
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.
B.
C.
D.
E.
F.
G.
H.
I.
Microarrays: expression profiling, RNA seq
Global Gene Knockouts
Global protein localization in yeast
Global complex identification in yeast
Global two-hybrid analysis in yeast and other organisms
RNAi
Transgenics, gene “knock-outs” (genetics not genomics)
Human Genome Project, Next Generation Sequencing,
and Comparative Genomics
ChIP for specific binding site, ChIP seq for all binding
sites throughout the genome
Science 296: 1661-1671
Human-Mouse comparison
Mouse
Genomic Synteny Map
Human
Alb 4-18
Synteny
Mouse Chr. 16Human
Comparison
Science 296: 1661-1671
31 May 2002
Human-Mouse Synteny
• Mouse chr. 16 =Human chr. 3, 8, 12, 16, 21, 22
• Mouse chr.16 - Human Gene comparison
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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 Neurons
Each Neuron makes ~1,000 connections
Total # 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”
Sp2
Sp3
Species 1
Mutation(s) and
Natural Selection
Darwin and Wallace: One Species Gives Rise to Another
Sp14
Sp4
Sp11 Sp12 Sp13 Sp7 Sp16 Sp17
Sp10
Sp12 Sp13
Sp9
Sp4
Sp5
Sp6
Sp2
Sp3
Sp7
Sp8
Species 1
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
Time = Mutations/(Mutation Rate)
Sp17
Phylogenetic Tree
Human-Chimp Divergence ~ 5,500,000 years ago
Within a Population (e.g. Humans)
Ind1
Ind2
Ind3 Ind4 Ind5 Ind6 Ind 7
Time = Mutations/(Mutation Rate)
Ind8
Within a Population (e.g. Humans)
Ind1
Ind2
Ind3 Ind4 Ind5 Ind6 Ind 7
Look at Mitochondrial Sequences: Maternal Lineage
Ind8
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
Y-chromosome Adam = 95,000 years ago in Sub-saharan Africa
~2,000 men left Africa 67,000 years ago
Ind8
Hartl6 16.5
Model from a Collection of Recent Data
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 interbred with Neanderthals in the Middle East -> People of European and Asian
descent have some Neanderthal alleles -> skin phenotypes: skin color and
keratin intermediate filaments
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?
Human Specific ASPM Allele
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!
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
10
14.5
Time
(Billions of Years)
10
20
Estimated Lifespan
of our Sun
What type of atoms were created in the big bang?
Timeline of the Universe and Earth
0
10
14.5
Time
(Billions of Years)
10
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…
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