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