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Before considering selection, it’s important to characterizehow gene expression varies within and between species.

What evolutionary forces act on gene expression regulation?

What facilitates regulatory evolution?

* Gene dispensibilityGenes with variable expression within species are heavily enriched for non-essential genes

* Genes with upstream TATA elementsTATA regulation in yeast (and other organisms?) is associatedwith variable expression

* RedundancyEither gene or regulatory redundancy

* Modularity in regulationGenes with more upstream elements or greater environmental responsiveness

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What contributes to the evolution of gene expression?

How many loci underlie expression variation?Few major effectors or many minor contributors?

What are the mechanisms of expression evolution?Relative prominence of cis vs. trans effects?

How much of expression variation has been selected for?

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eQTL mapping: understanding the genetic basis of expression variationfirst done in strains of yeast

From Rockman & Kruglyak 2006

First done by Rachel Brem et al.

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eQTL mapping in yeast spore clones

From Rockman & Kruglyak 2006

First done by Rachel Brem et al.

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LOD threshold in standard QTL mapping (* 1 trait)

•1000 permutations10% LOD score threshold: 3.195% LOD score threshold: 3.52

Challenge with eQTL mapping is that there are thousands of traits.

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Lessons for eQTL studies

• Only ~25% of heritable expression traits can even be mapped- on average they explain only 30% of heritable variation

• Most traits explained by many loci - only 3% explained by 1 locus- Alan Orr exponential QTL model: few big effectors with lots of modifiers

• Majority of traits explained by transgressive segregation

- distribution of F2 phenotypes extends beyond parental phenotypes

- indicates many small effectors

- suggests stabilizing selection

- also consistent with epistasis

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Lessons for eQTL studies

• Fewer traits showdirectional segregation

- Phenotypic distribution of F2’sbetween the parents

- Also implies many minoreffectors

- Suggests directional selectionby ‘tweaking’

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Local vs. Distant and cis vs. trans

ORF

Local QTL that work in cis:

TF binding siteaffects transcription

3’ UTRaffects RNA stability

Local eQTL: “near” the affected geneDistant eQTL: “far” from the affected gene

cis effect: often taken to mean on the DNA molecule affectedtrans effect: often taken to mean takes effect through the protein/RNA

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Local vs. Distant and cis vs. trans

Local eQTL: “near” the affected geneDistant eQTL: “far” from the affected gene

cis effect: often taken to mean on the DNA molecule affectedtrans effect: often taken to mean takes effect through the protein/RNA

ORF

Local QTL that work in trans:

Coding polymorphismthat affects TF activity

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Local vs. Distant and cis vs. trans

ORF

Distant QTL that work in trans:

Local eQTL: “near” the affected geneDistant eQTL: “far” from the affected gene

cis effect: often taken to mean on the DNA molecule affectedtrans effect: often taken to mean takes effect through the protein/RNA

ORF

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Local vs. Distant and cis vs. trans

ORF

Distant QTL that work in trans:

Local eQTL: “near” the affected geneDistant eQTL: “far” from the affected gene

cis effect: often taken to mean on the DNA molecule affectedtrans effect: often taken to mean takes effect through the protein/RNA

ORF

PHYSIOLOGY

Most trans acting effects are likely secondary responses(distantly-acting loci are NOT enriched for TFs)

Proportion of local versus distant linkages Transcriptabundance maps

to the genethat encodes it

Also see ‘hot spot’ locito where many transcripts map

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Local vs. Distant and cis vs. transWhich is more prevalent?

Estimates vary: - Brem et al papers: ~25% traits explained by local polymorphs

- other studies say close to 100%

- Many MORE individual genes explained by distant polymorphs* but because many link to same loci, there are

fewer distantly acting loci

But … statistical challenges likely enrich for local polymorphisms:

- FDR hurdle is higher for trans acting loci

- cis (local) polymorphisms may have larger effect size

- also depends on how “local” is defined

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Local vs. Distant and cis vs. transWhich is more prevalent?

Using hybrid diploids and allele-specific expression

ORF-1

ORF-2

A cis acting polymorphism will affect only the allele it’s physically linked to

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Local vs. Distant and cis vs. transWhich is more prevalent?

Using hybrid diploids and allele-specific expression

ORF-1

ORF-2

A trans acting polymorphism will affect BOTH alleles

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Local vs. Distant and cis vs. transWhich is more prevalent?

Tricia Wittkopp et al. 2004. Nature.

- 29 differentially expressed genes between D. melanogaster & D. simulans:

- Measured allele-specific expression in D. mel/D. sim hybrid with pyrosequencing

28 out of 29 show cis variation in expression

16 out of 29 affected by trans and cis variation

Conclusion: cis-acting variation is more common to explaininterspecific variation

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Local vs. Distant and cis vs. transWhich is more prevalent?

Tricia Wittkopp et al. 2008. Nature Genetics.

- 78 genes examined (48 within, 49 between species … 16 genes overlapping) 4 D. melanogaster strains and 4 D. simulans strains

Conclusion: trans-acting variation is more common within species (over shortertime frames) but is more likely to have more pleiotropic and deleterious effects

… trans-acting variation more likely to be removed over time

-cis regulatory effects explained more variationbetween (64%) species rather than within (35%)… argues against neutrality, since effects should occur

at same ‘rate’ over time

- compensatory cis + trans effects also more common between species