Questions• Are we ‘just’ E. coli, except more so?• Where do new genes come from?• Do all genes evolve at the same rate?• Do all tissues & organs evolve at the same rate?• Where do we fit in the tree of life?• What specifies the differences between us and

rodents, or us and chimps?• What specifies the elevated complexity of us versus

other animals?• Can we understand sequence variation among

humans?• How can gene function contribute to behaviour?

23 of 94 InterPro families: Defense and Immunitye.g. IL-1, interferons, defensins

17 of 94 InterPro families: Peripheral nervous systeme.g. Leptin, prion, ependymin

4 of 94 InterPro families: Bone and cartilageGLA, LINK, Calcitonin, osteopontin

3 of 94 InterPro families: LactationCaseins (), somatotropin

2 of 94 InterPro families: Vascular homeostasisNatriuretic peptide, endothelin

5 of 94 InterPro families: Dietary homeostasisGlucagon, bombesin, colipase, gastrin, IlGF-BP

18 of 94 InterPro families: Other plasma factorsUteroglobin, FN2, RNase A, GM-CSF etc.

‘New Domains’

Where do new genes come from?

Structure & Sequence

Sequence

Stepping through structure and sequence space:the FGF / IL-1 beta-trefoilstory

J Mol Biol. 2000 Oct 6;302(5):1041-7.

beta-trefoilsFGFs, interleukin-1s

FGF IL-1

EXTRACELLULAR (CELL-CELL SIGNALLING):

Fascin Hisactophilin

INTRACELLULAR (ACTIN-BINDING PROTEINS):

J.Mol.Biol. 302, 1041-1047

VERT., INVERT. VERT.

VERT., INVERT., FUNGI Dictyostelium.

Gene Genesis• Positive selection often leads to the

erosion of sequence similarity • If this erosion is extensive, homology

cannot be inferred from database search strategies.

• If, concomitantly, there is positive selection for duplication of these genes, this gives the appearance of a new gene/domain family that lacks antecedents.

Copley, Goodstadt, PontingCurrent Opinion in Genetics & Development Volume 13, December 2003, Pages 623-628

Conservation and Selection over Time

50.00%

60.00%

70.00%

80.00%

90.00%

100.00%

Con

serv

atio

n (%

iden

tity)

50% 100%

% o f o r th o lo g s fo u n d in fu g u

0 300150 450Tim e o f D iv e rg en ce (M y r)

M ouse-rat

Hum an-m ouseHum an-fugu

a

b

c

d

ef

hi

j

g

Cytoplasmic domainsNuclear domainsSecreted domains

0%

20%

40%

60%

80%

100%

0.00 0.10 0.20 0.30 0.40Per

ce

nta

ge

of

se

qu

en

ces

K /KA S

Do all tissues & organs evolve at the same rate?

PNAS | April 2, 2002 | vol. 99 | no. 7 | 4465-4470 Genetics

Large-scale analysis of the human and mouse transcriptomes Andrew I. Su et al.

http://expression.gnf.org

Need to investigate expression of tissue-specific genes.

• Tissue Specificity of a Gene: TS

• A gene's fractional expression in a tissue relative to the sum of its expression in all tissues

• max TS : an indicator of Tissue Specificity.

• Divide data into 5 sets:

• (1) maxTS ≤ 0.1;

• (2) 0.1 < maxTS ≤0.2;

• (3) 0.2 < maxTS ≤ 0.3;

• (4) 0.3 < maxTS ≤ 0.4;

• (5) maxTS > 0.4

All

Non-secreted

Secreted

Non-disease

Disease

Protein secretionaccounts for much ofthe elevation in KA /KS

for Tissue-Specific genes.

Eitan Winter

Slow Fast

Brain Blood

Kidney

Thymus

Liver

(KA/KS=0.04) (KA/KS=0.13)Evolutionary Rates

Low High

Brain Blood

Kidney

Trachaea

Liver

(12.2%) 50%Protein Secretion (%)

Testis

All

Non-secreted

Non-disease

Disease

Secreted

Housekeeping genesare under-representedamong disease genes

Eitan Winter

Low High

Brain Blood

Kidney

Trachaea

Liver

(5.0%) 39%Human Disease (%)

Testis

Tissue-specific genes’ Ks

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8M

ed

ian

Ks

-va

lue

Winter et al. Genome Research 14:54-61, 2004

Tissue/Organ Evolution

• Mammalian tissues & organs are evolving at different rates, according to the genes that are specifically expressed in them.

• Perhaps this is not too surprising since there are mammalian-specific tissues & organs!

• Tissue-specific genes are ‘mutating’ at different rates, possibly due to transcription-coupled repair in the germline.

• Mendelian disease acts non-uniformly among genes and tissues.

Human-Mouse Orthologues’ Expression Profile Correlations

0

2

4

6

8

10

12

14

16

18

-1 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Pearson Correlation

%

Orthologue Pairs

Random Pairs

EitanWinter

Pan troglodytes genome

• 4X coverage

• average nucleotide divergence of just 1.2%

How do the 2 gene complements differ?

• Gene duplications observed in the human genome.

• Lack of N-glycolylneuraminic acid (Neu5Gc) in humans due to mutation in CMP-sialic acid hydroxylase (Chou et al. PNAS 95(20):11751-6.)

• Mutation in a Siglec (sialic acid receptor) (Angata et al. JBC 276:40282-7)

How do the Great Apes differ from us?

• Rare HIV progression to AIDS• Resistant to malarial infection• Menopause rare• Coronary atherosclerosis rare• Epithelial cancers rare• Alzheimer’s disease pathology incomplete

FOXP2• A point mutation in FOXP2 co-segregates with a disorder in a family in

which half of the members have impaired linguistic and grammatical abilities

• Human FOXP2 contains missense mutations and a pattern of nucleotide polymorphism, which strongly suggest that this gene has been the target of selection during recent human evolution. Enard et al. Nature 418, 869 - 872

Figure 2 Silent and replacement nucleotide substitutions mapped on a phylogeny of primates. Bars represent nucleotide changes. Grey bars indicate amino acid changes. P < 0.001

Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.

PLoS Biol. 2004 Jan;2(1):E5. Epub 2004 Jan 20 Gilad et al.

Figure 2. The Proportion of OR Pseudogenes in 20 Species

Table 1. Biological processes showing the strongest evidence for positive selection. The top panel includes the categories showing the greatest acceleration in human lineage, and the bottom panel includes categories with the greatest acceleration in the chimp lineage.

Biological process Number of

genes* PMW (human/Model

2)* PMW (chimp/Model

2)*

Categories showing the greatest acceleration in human lineage

Olfaction 48 0 0.9184 Sensory perception 146 (98) 0 (0.026) 0.9691 (0.9079) Cell surface receptor—mediated signal transduction

505 (464) 0 (0.0386) 0.199 (0.0864)

Chemosensory perception 54 (6) 0 (0.1157) 0.9365 (0.7289) Nuclear transport 26 0.0003 0.2001 G protein—mediated signaling 252 (211) 0.0003 (0.1205) 0.2526 (0.0773) Signal transduction 1030 (989) 0.0004 (0.0255) 0.0276 (0.0092) Cell adhesion 132 0.0136 0.3718 Ion transport 237 0.0247 0.8025 Intracellular protein traffic 278 0.0257 0.8099 Transport 391 0.0326 0.7199 Metabolism of cyclic nucleotides 20 0.0408 0.1324 Amino acid metabolism 78 0.0454 0.0075 Cation transport 179 0.0458 0.8486 Developmental processes 542 0.0493 0.2322 Hearing

21

0.0494

0.9634

Categories with the greatest acceleration in the chimp lineage

Signal transduction 1030 (989) 0.0004 (0.0255) 0.0276 (0.0092) Amino acid metabolism 78 0.0454 0.0075 Amino acid transport 23 0.1015 0.0102 Cell proliferation and differentiation 82 0.3116 0.0182 Cell structure 174 0.2633 0.0233 Oncogenesis 201 0.3132 0.0267 Cell structure and motility 239 0.2208 0.0299 Purine metabolism 35 0.9127 0.0423 Skeletal development 44 0.2876 0.0438 Mesoderm development 168 0.5813 0.0439 Other oncogenesis 39 0.2777 0.0469 DNA repair

49

0.9363

0.0477

* The number of genes and the PMW values excluding olfactory receptor genes are shown in

Clark et al.Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios Science (2003) 302: 1960-1963

Table 2. Molecular functions showing the strongest evidence for positive selection. The table includes only human-accelerated categories, because the only categories accelerated in the chimp lineage are chaperones (P = 0.0124), cell adhesion molecules (P = 0.0220), and extracellular matrix (P = 0.0333).

Molecular function Number of

genes* PMW (human/Model

2)* PMW (chimp/Model

2)*

G protein coupled receptor 199 (153) 0 (0.2533) 0.8689 (0.6776) G protein modulator 62 0.0008 0.3776 Receptor 448 0.0030 0.9798 Ion channel 134 0.0043 0.8993 Extracellular matrix 97 (95) 0.0120 (0.0178) 0.1482 (0.1593) Other G protein modulator 32 0.0149 0.4441 Extracellular matrix glycoprotein

44 (42) 0.0178 (0.0269) 0.1579 (0.1765)

Voltage-gated ion channel 62 0.0219 0.6692 Other hydrolase 95 0.0260 0.4823 Oxygenase 46 0.0303 0.4792 Protein kinase receptor 37 0.0314 0.6911 Transporter 214 0.0338 0.1836 Ligand-gated ion channel 45 0.0405 0.9503 Microtubule binding motor protein

22 0.0421 0.6385

Microtubule family cytoskeletal protein

54

0.0467

0.2815

* The number of genes and the PMW values excluding olfactory receptor genes are shown in parentheses.

• “Smell, Hearing Genes Differ between Chimps and Humans” Genome News Network January 9 2004

• “The 2.5Gb mouse genome sequence reveals about 30,000 genes, with 99% having direct counterparts in humans.”

Nature editorial 5 December 2002.

Questions• Are we ‘just’ E. coli, except more so? Not at all.• Where do new genes come from? Old genes!• Do all genes evolve at the same rate? No.• Do all tissues & organs evolve at the same rate? No.• Where do we fit in the tree of life? Primates!• What specifies the differences between us and

rodents, or us and chimps? Jury is out. Duplicates?• What specifies the elevated complexity of us versus

other animals? Jury is out.• Can we understand sequence variation among

humans? Not yet – Lon’s lecture?• How can gene function contribute to behaviour?

Seen in rodents, but not yet in primates.

Near Future

Genome Sequencing Capacity (NHGRI)

YEAR 7X genome

(3 Gb)

1X genome

(3 Gb)2003 2.5

genomes18

genomes

2004 4.9 genomes

34 genomes

2005 6.2 genomes

43 genomes

2006 8.4 genomes

59 genomes

Sampling the placental mammalphylogeny

(Murphy et al. Science 2001 294: 2348-51 )

*

*

MRC Functional Genetics Unit, Oxford

Leo GoodstadtRichard EmesEitan WinterSteve Rice

Scott BeatsonNick Dickens

Caleb WebberMichael Elkaim

Jose DuarteZoe BirtleTania Oh

Ensembl (Ewan Briney, Michele Clamp, Abel Ureta-Vidal);Richard Copley (WTCHG, Oxford); Ziheng Yang (UCL);

The Human, Mouse and Rat Genome Sequencing Consortia; UCSC

BibliographyHuman Genome Papers:

Lander et al. Nature (2001) 409, 860-921

Venter et al. Science (2001) 291, 1304-1351.

Mouse Genome Paper:

Waterston et al. Nature (2002) 420, 520-62.

Rat Genome Paper: submitted.

Comparative genomics & evolutionary rates:

Hardison et al. Genome Res. (2003) 13, 13-26.

Adaptive evolution of genomes:

Emes et al. Hum Mol Genet. (2003) 12, 701-9

Wolfe & Li Nat Genet. (2003) 33 Suppl: 255-65