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Evolutionary changes in cis and trans gene regulation


Differences in gene expression are central to evolution. Such differences can arise from cis-regulatory changes that affect transcription initiation, transcription rate and/or transcript stability in an allele-specific manner, or from trans-regulatory changes that modify the activity or expression of factors that interact with cis-regulatory sequences1,2. Both cis- and trans-regulatory changes contribute to divergent gene expression, but their respective contributions remain largely unknown3. Here we examine the distribution of cis- and trans-regulatory changes underlying expression differences between closely related Drosophila species, D. melanogaster and D. simulans, and show functional cis-regulatory differences by comparing the relative abundance of species-specific transcripts in F1 hybrids4,5. Differences in trans-regulatory activity were inferred by comparing the ratio of allelic expression in hybrids with the ratio of gene expression between species. Of 29 genes with interspecific expression differences, 28 had differences in cis-regulation, and these changes were sufficient to explain expression divergence for about half of the genes. Trans-regulatory differences affected 55% (16 of 29) of genes, and were always accompanied by cis-regulatory changes. These data indicate that interspecific expression differences are not caused by select trans-regulatory changes with widespread effects, but rather by many cis-acting changes spread throughout the genome.

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Figure 1: Pyrosequencing8 measures allelic gene expression.
Figure 2: Cis-regulatory changes frequently contribute to interspecific expression differences.
Figure 3: Evolutionary changes in both cis- and trans-regulation underlie interspecific expression differences.
Figure 4: Models of regulatory divergence.


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We thank A. Kumari and S. Madhavarapu for experimental assistance, K. Montooth for statistical advice, and K. Montooth, B. Payseur, A. Fiumera, T. Schlenke and E. Hill for comments on the manuscript. Funding for this project was provided by NIH grants to A.G.C. P.J.W. is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation, and B.K.H. was funded by a Howard Hughes Undergraduate Research award.

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Correspondence to Patricia J. Wittkopp.

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Supplementary information

Supplementary Notes

This file describes: (1) comparisons of the genes analyzed to genomic microarray data, and (2) rationale for our cDNA normalization method. (DOC 994 kb)

Supplementary Figure 1

This figure demonstrates that Pyrosequencing accurately measures allele frequency. (DOC 99 kb)

Supplementary Figure 2

This figure shows that the parent-of-origin had little effect on allelic expression in F1 hybrids. (PDF 66 kb)

Supplementary Figure 3

This figure summarizes the normalized mean cDNA ratios for each pool analyzed. (DOC 434 kb)

Supplementary Table 1

This table lists the available Gene Ontology annotations of molecular function for the genes analyzed. (XLS 29 kb)

Supplementary Table 2

This table includes means, confidence intervals, and exact P-values for all statistical analyses. (XLS 32 kb)

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Wittkopp, P., Haerum, B. & Clark, A. Evolutionary changes in cis and trans gene regulation. Nature 430, 85–88 (2004).

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