Genetics of Gene Expression

Chris Cotsapascotsapas@broad.mit.edu

Outline

Background Significance Experimental design Definitions

Basic findings Tissue specificity Population differences Biological insight (?) Last thoughts

In the beginning...

King and Wilson, Science 1975 Chimp – human coding sequence differences

don't match phenotypic distance Gene regulation responsible for rest? Basis for evo-devo, GGE

Genetics of gene expression

Find genetic variation that (partially) controls levels of RNA

If RNA levels are different, maybe protein levels are also different

If protein concentration is different, maybe there is a phenotype?

Experimental design

Protein measurements 2D gels; quantitation hard; resolution?

RNA measurements Expression chips ca. 1995 (Schena et al, Science)

Experimental design - methods

Allelic discrimination SBE Pyrosequencing SNP arrays

Whole-genome expression assays Genotypes?

Experimental design - samples

Pedigrees – multiplex/trios HapMap

Population samples Inbred strain panels

genotypes New crosses Inter-specific hybrids

Definitions

Cis

Trans

Outline

Background Basic findings Tissue specificity Population differences Biological insight (?) Last thoughts

First forays

Damerval et al 1994 Protein levels are different in 42/72 maize gene

products 2D electrophoresis, eyeball spot quantitation Problems:

genome coverage quantitation post-translational modifications

Cowles et al 2002

F1 mice 69 genes in three tissues 4 variant; 2 only in liver

Yeast WG approaches

Brem et al Science 2002 Linkage in 40 offspring of lab x wild strain cross 1528/6215 DE between parents 570 map in cross

multiple QTLs 32% of 570 have cis linkage

262 not DE in parents also map

Trans hotspots

Brem et al Science 2002

Yvert et al Nat Genet 2003

Mammals I

F2 mice on atherogenic diet Expression arrays; WG linkage

Schadt et alNature 2003

Mammals II

Chesler et al Nat Genet 2005

10% !!

Mammals III

No major trans loci in humans Cheung et al Nature 2003 Monks et al AJHG 2004 Stranger et al PLoS Genet 2005, Science 2007 Further scans (WT, Cheung, Schadt etc)

What's the deal with trans?

Artefacts Normalization robustness Replication? Clusters of correlated genes

Power trans often weak effects Small sample sizes

Outline

Background Basic findings Tissue specificity Population differences Biological insight (?) Last thoughts

trans-acting factors may be tissue specific TFs, signalling molecules, etc etc

cis regulatory sequences may be used by TS factors

So, shouldn't genetic effects on GE be tissue specific?

Logic

Examples

Chesler vs Bystrykh (Nat Genet 2005) 39/101 (39%) forebrain cis in HSC 297/1218 (24%) HSC cis in forebrain

Hubner (Nat Genet 2005) 311/4297 (7%) shared between fat and kidney

Campbell et al (Gen Res 2008) 12% of ~100 genes vary in at least one of three

tissues

Correlation networks persist across tissues

Outline

Background Basic findings Tissue specificity Population differences Biological insight (?) Last thoughts

Slide courtesy Alkes Price

Population differences could have non-genetic basis

• Differences due to environment? (Idaghdour et al. 2008)

• Differences in cell line preparation? (Stranger et al. 2007)

• Differences due to batch effects? (Akey et al. 2007)

(Reviewed in Gilad et al. 2008)

Slide courtesy Alkes Price

Gene expression experiment

Does gene expression in 60 CEU + 60 YRI vary with ancestry?

Does gene expression in 89 AA vary with % Eur ancestry?

60 CEU + 60 YRI from HapMap, 89 AA from Coriell HD100AAGene expression measurements at 4,197 genes obtained using Affymetrix Focus array

c

Slide courtesy Alkes Price

Gene expression differences in African Americans validate CEU-YRI differences

c = 0.43 (± 0.02)(P-value < 10-25)

12% ± 3%in cis

Slide courtesy Alkes Price

Outline

Background Basic findings Tissue specificity Population differences Biological insight Last thoughts

Does GGE matter?

Where is the phenotype? Case/control differences?

Does it translate to protein? Can we reconstruct networks/pathways?

Insight

Mechanism? trans – coregulated groups?

pathways Model QTs Molecular variation snapshots

What does it mean? Ancillary information

IRGM harbors a 20-kilobase deletion polymorphism immediately upstream

CEU 0.06 1.0

J CH 0.41 1.0

YRI 0.53 1.0

Deletion allele

frequency

LD (deletion,

rs13361189)

IRGM

Ind

ivid

ua

ls

Position on chr5

rs13361189(strongest Crohn’s-associated SNP)

Slide courtesy Steve McCarrollMcCarroll et al., Nature Genetics, Sept. 2008

Slide adapted, courtesy Steve McCarroll

IRGM structural haplotypes have altered expression

McCarroll et al., Nature Genetics, Sept. 2008

IRGM expression levels influence the efficacy of autophagy

McCarroll et al., Nature Genetics, Sept. 2008 Slide adapted, courtesy Steve McCarroll

Outline

Background Basic findings Tissue specificity Population differences Biological insight (?) Last thoughts

Success?

Baseline variation - tricky Perturbations and phenotypes

mouse obesity crosses (Schadt et al) Drug screening (Choi, Yelensky et al) Crohn's disease (McCarroll et al)

Stuff we haven't covered

Coregulated sets Disease context Annotation/pathway analysis Modelling QTLs Regression WGAS Multiple data sets/types Post-transcriptional event variation