What can cause expression level differences?
cis - change in regulatory sequence (promoter) linked to target gene
trans - change in different, unlinked gene (TF) that affects expression of target gene
What mainly causes expression differences?
mainly by cis change, but trans also frequently involved
in experiment of D. melanogaster and D. simulans:
50% of genes —> cis
50% of genes —> cis and trans
What is Allele Specific Expression (ASE)
expression differencs between parents caused by cis
—> 2 alleles should expressed differently and match expression difference of parents
What is the best example for “evolution in action”?
Insecticide resistance
since 1940s used insecticides (DDT)
typically insects rapdily evolve resistance (not only in target species)
possible to map and identify genes responsible for DDT-resistance (DDT-R)
To what was DDT-R mapped to in D. melanogaster?
DDT-R mapped to cytochrome P450 gene, Cyp6gl
What is Cytochrome P450?
large family of related genes (≈90) involved in metabolism of many compounds
What is different in DDT-R flies to DDT-S flies?
DDT-R flies
have TE insertion at 5’ end of Cyp6gl gene
higer expression of Cyp6gl gene
DDT-S flies
no TE insertion
—> suggests that TE insertion increases gene expression —> leads to DDT resistance
What is Population Transcriptomics?
comparison of global gene expression levels among individuals from natural populations of species
= combination of population genetics and transcriptomics
What are some Transcriptomic methods?
microarrays
RNA-seq
—> allow large-scale quantitative measurement of phenotypes
Why is gene expression sometimes considered as “intermediate phenotype”?
it lies between genotype and organismal phenotype that ultimately responds to selection
How should be DNA sequence polymorphism in gene be affected, if expression divergence of gene between African and European flies is result of recent adaptive cis-regulatory evolution?
DNA seq polymorphism reduced in one of populations
-> producing signal of ‘selective sweep’
one/more fixed seq differences between populations
-> polymorphism high frequency in one, low in other population
What is the role of MtnA compared between African and European flie?
= brain transcriptome
more expression differneces in brain between populations than between sexes
most genes differend in expression -> showed same pattern in both sexes
—> expression difference: by deletion of negative regulatory element in MtnA 3’ UTR (binding site for microRNA?)
CG9509 (aka fezzik) between African and European fly?^
consistenltly shows 2-3 times higher expression in non-African than in African flies
—> absence of sequence polymorphism in genomic region just upstream of CG9509 in European
tested with reporter genes
What are the predicted functions of CG9509?
encode choline dehydogenease enzyme
involved in ecdysteroid metabolism (growth hormone)
expressed in Malphigian tubules (kidneys)
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