evolution of gene expression

cis: change in regulatory sequence linked to the target gene (eg promoter, enhancer)

trans: change in a different, unlinked gene different, (eg a transcription factor) that affects expression of the target gene

2004

use 2 fly species (melanogaster, simulans) with expression differences in a gene

• make F1 hybrid

• use pyrosequencing to meassure the expression of individual alleles

• also later possible with NGS

Exprected results:

• if trans: in hybrid the two alleles should have equal expression (trans factors can reach both)

• is cis: 2 alleles in hybrid should have different expressions = Allele-Specific Expression

• if ONLY cis: match parant expressions, else, lie between

Results observed:

• 28/29 genes showd different expressions btw the alleles

• 50% of these had additional trans changes

-> Gene expression changes btw species mainly due to cis, but trans is also involved

mainly by cis, how much trans contributes relatively, depends on the environmental conditions (media)

a cytochrome P450 gene (Cyp6g1)

-> large family of 90 related genes involved in metabolism

in DDT-R: TE insertion in 5’ end of Cyp6g1

-> higher expression of the Cyp6g1

-> TE insertion is beneficial and drives adaptive evolution

pop gen + transcriptomics

comparison of global gene expression levels among individuals from different populations, of the same species

= gene expression

• because between genotype and organismal phenotype

• because it is not the level thing resopnding to selection, that is the organismal phenotype

DNA seq polymorphism in gene or near gene should be affected

• Reduced in min 1 of the 2 pops = signal of selective sweep

• at least one (nearly) fixed variant in min 1 of the 2 pops

  (=polym. at high frequency in 1, low/absent in the other )

brain: more differences btw pops

whole flies: more differences btw sexes

MtnA, metallothionein gene

-> heavy metal deoxification and oxidative stress tolerance

Deletion of a negative reulatory element in 3’UTR, may be binding site for microRNA

-> Higher MtnA expression

-> Del at HIGH freq ooA -> in europe (posotive selection in european populations, flies are from africa)

metallothionein

-> heavy metal detoxification and oxidative stress tolerance

• the further away from equador, the higher becomes the frequency of the Delition variant

• however NOT fixed, suggestive of trade off (subject to balancing selection?)

absence of seq Polymorphism upstream of the gene in european pop, several fixed sequence differences

There is a non coding snp in cis

-> leading to increase in epression, favourable in european population

-> in vitro experement shows: Fully due to cis regulatory divergence

in vitro:

use reporter gene containing the upstream region of african Or european allele, put in E. Coli lac Z gene

then, insert into fly using PhiC31 site-specification, into uptream region

-> compare effect of both upstream regoins in same genetic background

-> If there is a difference in expression between the two reporter genes, then it must be the result of cis-regulatory divergence

here, fully cis-regulatory as 2-3 higher expression observed

• SNP with greatest effect: not fixed, but 0.45 in eu and 0.025 in aftrican -> balancing selection, not a selective sweep

exact function unknown

• prediction: encode chlorine dehydogenase enzyme

• involved in scdysteroid metabolism = growth hormone

• expressed in kidney analogs: Malphigian tubules

• influence on growth and stress tolerance

• larger flies

• name of gene fezzik: a giant character in the princess bride

• more trans than cis factors

• enrichment in cis variantion in cytochrome p450 genes

• most cis-variants in P450 geneswere located in the region just upstream of the gene (within 2 kb of the start codon)