V.7 Evolution of Gene Expression Patricia J.Wittkopp OUTLINE of a gene and that has allele-specific effects on gene expression. 1. The importance of regulatory evolution: a Co-option. Using existing functional parts of a genome historical perspective for new purposes. 2. Finding expression differences within and Ectopic Expression. Expression in cells that do not usu- between species ally express the gene of interest. 3. Genomic sources of regulatory evolution Orthologous Genes. Homologous genes that diverged 4. Enhancer evolution following a speciation event. 5. Evolution of transcription factors and Pleiotropy. Occurs when a mutation or gene affects more transcription factor binding than one phenotype. 6. Evolutionary forces responsible for expression Quantitative Trait Locus (QTL). Aregionofthegenome divergence shown to influence a (quantitative) phenotype of interest. Genetic changes affecting either the function or regu- RNA Interference (RNAi). A technique in which short RNAs lation of a gene product can contribute to phenotypic are used to interfere with the successful production of evolution. Studies of evolutionary mechanisms have his- proteins for a gene of interest. torically focused on changes in protein-coding sequen- Transcription Factor. A protein that binds to DNA in a ces, but during the last decade, multiple lines of evidence sequence-specific manner and affects transcription. have shown that changes in gene expression are at least equally important. The last few years have brought great progress in understanding the genetic basis of expression 1. THE IMPORTANCE OF REGULATORY EVOLUTION: differences within and between species. From a growing A HISTORICAL PERSPECTIVE collection of single-gene case studies and comparative analyses of gene expression on a genomic scale, common For most of the twentieth century, conventional wis- themes and patterns in regulatory evolution have begun dom among biologists was that, as Franc¸ois Jacob to emerge. described it, “cows had cow molecules and goats had goat molecules and snakes had snake molecules, and it GLOSSARY was because they were made of cow molecules that a cow was a cow.” Near the end of the twentieth century, Chromatin. The higher-order complex of DNA, histones, however, it became clear that this was not the case. and other proteins that packages nuclear DNA within Species-specific genes exist (see chapter V.6), but they a eukaryotic cell. are the exception rather than the rule; much of the Chromatin Immunoprecipitation. A technique in which biological diversity seen in nature is produced by genes transcription factors are cross-linked to DNA, the whose functions are highly conserved among species. DNA is sheared, and fragments binding to a specific Discovering this conservation was a boon to the med- transcription factor of interest are isolated using an ical genetics community, because it justified the use of antibody. Identity of the isolated DNA fragments model organisms such as fruit flies and mice to in- can be assessed by PCR, microarrays, or sequencing. vestigate human disease, but also presented a paradox: cis-regulatory Element. A DNA sequence (such as an how can divergent traits be constructed using con- enhancer or promoter) located near the coding region served genes? 414 Genes, Genomes, Phenotypes The answer to this question is, in part, by modifying still are) critical for establishing links between divergent the regulation of gene expression. Expression of a gene is gene expression and divergence of a particular pheno- necessary before it can impact the phenotype of an or- type; however, they are not suitable for obtaining the ganism; that is, the DNA sequence encoding a gene prod- genomic measures of expression required to identify uct must be transcribed into RNA and then (usually, but global trends in the evolution of gene expression. Ra- not always) translated into a protein before the gene can ther, microarrays, which are short DNA sequences com- function in a cell. Each cell expresses only a subset of the plementary to transcribed sequences from a particular genes in its genome, and the specific genes expressed species arrayed onto a filter or a microchip, have been determine a cell’s fate (see chapter V.11). In 1969, before used to quantitatively compare the abundance of RNA the molecular details of gene regulation were known, from hundreds to thousands of expressed genes in the Roy J. Brittan and Eric H. Davidson proposed a theory genome simultaneously. Today, microarrays are largely for the regulation of gene expression in eukaryotic cells. being replaced by a method known as RNA-seq that uses They viewed gene regulation as integral to evolution and massively parallel sequencing to obtain quantitative mea- suggested that differences among species could be at- sures of gene expression (i.e., RNA abundance). Tech- tributable to changes in the regulation of gene expres- niques for measuring protein abundance (which is not sion. Six years later, Mary-Claire King and A. C. Wilson always highly correlated with RNA abundance) on a ge- published a seminal paper showing that the amino acid nomic scale are also available (e.g., two-dimensional gel sequences of homologous human and chimpanzee pro- electrophoresis, mass spectrometry), but thus far they teins appeared to be more than 99 percent identical. have not been used to compare protein expression gen- Based on this result, they argued that the degree of pro- ome-wide in an evolutionary context. tein divergence was insufficient to account for the ex- By contrast, the transcriptome (i.e., the collection of tensive morphological, physiological, and behavioral all RNAs expressed in a biological sample) has been differences between these two species. analyzed in a wide variety of taxa, including human, Despite these (and similar) predictions more than 35 mice, fishes, flies, yeast, and plants. Comparing tran- years ago, the idea that changes in gene expression might scriptomes has shown that differences in RNA abun- be a common source of phenotypic divergence did not dance are common both within and between species and gain mainstream acceptance among evolutionary biol- that the number of genes showing expression differences ogists until after the turn of the twenty-first century. between a pair of species is often proportional to their Seeds of this acceptance were sown when developmental divergence time. For example, in one of the first pub- biologists, using newly developed tools for visualizing lished transcriptome comparisons between species, mi- gene expression, began comparing expression among croarrays containing sequences complementary to ap- species. This approach catalyzed the expansion of evolu- proximately 12,000 human genes were used to measure tionary developmental biology, a field of research known mRNA abundance in white blood cells, liver, and brain today as evo-devo. Within a few years, researchers ac- of humans, chimpanzees, orangutans, and macaques. quired many examples of cases in which divergent RNA Comparing expression in samples from three humans, and/or protein expression of genes known to be im- three chimpanzees, and one orangutan showed exten- portant for development correlated with morphological sive variation within both humans and chimpanzees. divergence between species. Such correlations suggest The extent of expression divergence between humans that the genetic changes responsible for altered gene ex- and chimpanzees was smaller than the divergence ob- pression might be the same changes responsible for al- served when either of these species was compared to the tered phenotypes. In parallel, quantitative geneticists orangutan, suggesting that expression divergence cor- mapping the mutations responsible for phenotypic dif- relates with phylogenetic distance. In the samples de- ferences among individuals of the same species or (less rived from brains, one human was found to differ more commonly) different species were finding that changes in from another human than from a chimpanzee, but this protein sequence could not always account for the phe- type of relationship is rare: polymorphic gene expression notypic effect of a quantitative trait locus (QTL) (see within a species is typically less extensive than divergent chapter V.12). gene expression between species. In a slightly different experiment, macaques were 2. FINDING EXPRESSION DIFFERENCES WITHIN used as an outgroup, and gene expression in humans was AND BETWEEN SPECIES found to have evolved faster in the brain than in the liver or blood. Although it is tempting to speculate that this Early comparative studies of gene expression focused on apparently accelerated evolution of gene expression in one or a small number of genes within or between spe- the human brain may have contributed to the evolu- cies. These low-throughput types of studies were (and tion of human-specific cognitive abilities, a reanalysis of Evolution of Gene Expression 415 these data that more completely modeled the sources of a particular place, time, or environment. Because of their variance in the experiment found more genes with dif- more limited effects on an organism (i.e., lower pleio- ferential expression in the liver than in the brain between tropy), enhancers are commonly thought to be more humans and chimpanzees. This example illustrates the likely to harbor mutations that survive in natural po- potential tremendous impact of statistical analysis me- pulations and give rise to polymorphism and divergence thods on the conclusions drawn from