cis-trans compensation - senecio7の日記

Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG & Hartl DL 2005 Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171:1813-1822.

cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements
such coevolution should often lead to gene misexpression in the hybrid
we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F₁ hybrid
13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid
these represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species

through the process of natural selection, genes within a genome become coadapted (Dobzhansky 1937)
the extent of genomic coadaptation within species can be measured ex post facto by disrupting the harmonious genetic background
a classical example is the production of novel phenotypes in hybrids between species, which is thought to result, at least in part, from combinations of incompatible gene products encoded by the respective genomes now present in the same cells

numerous genes with expression levels in F₁ hybrids that are completely outside the range of that found in the parental species
these observations support the hypothesis of pervasive coadaptation of genetic regulatory elements
the reasons for the hybrid misexpression are unclear

the hypothesis of cis × trans interaction at individual genes, however, can be subjected to a rigorous experimental test

the regulation of gene expression requires the harmonious interaction of trans-regulatory elements (in the simplest case, transcription factors) with cis-regulatory elements (in the simplest case, DNA-binding sites for the transcription factors)
if natural selection acts to maintain an optimal level of gene expression through time (stabilizing selection), as it appears to (Denver et al. 2005; Lemos et al. 2005), then genetic changes in cis- and trans-regulatory elements that compensate each other may accumulate
consequently, regulatory elements may diverge genetically between species even though the level of gene expression remains approximately constant

compensated cis- and trans-regulatory evolution between species is a manifestation of a process coined developmental-system drift by True and Haag (2001)
through which the phenotypes are evolutionarily maintained despite a turnover of the underlying developmental networks

when the cis-regulatory divergence between alleles detected in the hybrid background is larger than the divergence between species, we can infer that there is also divergence in trans that compensates the changes in cis to bring the level of expression of the gene to a more similar level between species than expected given the divergence in cis
an extreme example of this scenario would be when the allelic divergence in the hybrid is in the opposite direction to the species divergence

for roughly one-third of the genes, the alleles differed in their expression to a smaller extent between the parental species than in the hybrids (Wittkopp et al. 2004)

to test for cis-trans-regulatory coadaptation that would result in misexpression, it is necessary to assay the total levels of gene expression in hybrids and the parental species, as well as the ratio of expression of the parental alleles in the hybrid background

gene expression analysis:
we measured the total level of expression in hybrids relative to that in the parental strains using quantitative real-time PCR (methods shown below) and measured allele-specific expression in hybrids and parental species using pyrosequencing
only 4 of the 8 selected genes showed patterns consistent with compensatory cis-trans regulation (6 of 8 still show divergence in cis) at this later stage

allele-specific gene expression level:
for all of the 31 genes, pyrosequencing was used to measure allele-specific gene expression as described in Witkopp et al. (2004)
pyrosequencing uses a single-nucleotide difference in the transcribed sequence to measure the relative expression of two alleles in the same sample
the relative expression levels of D. melanogaster and D. simulans alleles were determined by calculating the ratio of species-specific nucleotide incorporation at the divergent site

tests were for
(1) no differential expression in the parents (P-ratio = 1)
(2) no differential expression in the hybrid (H-ratio = 1)
(3) ratio of allelic expression in the parental lines equals that in the hybrid (P-ratio = H-ratio)

these null hypotheses correspond, respectively, to
(1) no expression difference between the parental species
(2) no difference in cis-regulatory elements
(3) no difference in trans-regulatory elements

pyrosequencing appears to be better able to detect small differences than microarrays
probably because of the large number of replicates or perhaps because DNA microarrays are inherently noisier

we hypothesized that compensatory cis-trans regulatory evolution within species should often result in misexpression in the interspecific hybrid owing to incompatibilities in the regulatory systems
the goal was to determine what fraction of genes, if any, that exhibited misexpression in F₁ hybrids showed a pattern of allelic expression consistent with cis-trans compensatory regulation

compensatory evolution can therefore occur at the cis-cis-, trans-trans-, and cis-trans-regulatory levels
the relative importance of each of those levels of interaction cannot be determined using our approach
because we concentrated on cases where there is cis-regulatory divergence

it is also impossible to determine from the patterns of expression if the changes in trans affect the transcription factors themselves, such as changes in the protein sequences, or other trans-regulatory effects such as the concentration of transcription factors or of other effects
the contribution of protein sequence variation of transcription factors to genetic variation in gene expression is largely unknown