Evolution of gene regulation

We study the evolution of gene regulation, seeking to uncover the general rules that govern changes in transcriptional machinery. This is important for two reasons. It helps to understand how complex molecular machines evolve. It also informs comparative genomics, an effort to infer biological functions from genome comparisons. Research in model organisms guides progress in other species, including humans, where many experiments are simply not possible (Romero et al. 2012).

We discovered a new mechanism that ensures robust (i.e. relatively insensitive to perturbations) gene expression. We dissected the regulatory element of a gene and found that it consists of two parts— the proximal, sufficient to direct the spatial expression pattern, and the distal, whose function is to maintain constant levels of expression under different environmental conditions (via open chromatin). This distal robustness element relies only on general sequence composition (AT-enrichment), not specific motifs, and therefore has evolved quickly, unlike the proximal promoter, which is under strong selective constraint. This research reveals how regulatory precision and robustness are achieved through distinct molecular mechanisms with equally distinct signatures of molecular evolution (Barrière et al. 2011).

We gained insights into the relationship between functional conservation of cis elements and their sequence conservation. We found that conserved expression pattern of a gene could persist during evolution despite functional divergence of both cis elements and transcription factors. Even more unexpectedly, we showed that a promoter of a gene could experience an accelerated rate of sequence evolution in one species, and yet drive expression in the same pattern as its slowly-evolving homologs in other species (Barrière et al. 2012). Fast-evolving regulatory sequences are often thought to be associated with genes that acquired new species-specific functions, including in humans. Our results suggest that care must be taken when making inferences of function based on sequence comparisons.

To assess whether general rules governing change in gene-regulaotry mechanisms could be discovered, we analyzed over 100 studies that compared the functions of regulatory elements from different species (Gordon and Ruvinsky 2012). Common patterns emerge with surprising consistency, implying that a unified view of regulatory evolution can be obtained.

We tested inferences of this meta-analysis. We showed that cis-elements of fly and human heat-shock genes are induced in C. elegans upon exposure to heat, albeit in incorrect spatial patterns, arguing that some aspects of regulation are retained over longer periods of evolutionary time than others (He et al. 2011). Second, cis-elements from nematodes that diverged 400 million years ago still have the ability to direct surprisingly faithful expression patterns in C. elegans, despite having retained no discernible sequence homology. This proves that the regulatory logic, i.e. transcription factors that control expression, can be preserved, even though cis-elements changed beyond recognition (Gordon et al. 2014). Finally, cis-elements of genes from closely related nematodes show widespread functional divergence in gene regulatory mechanisms, but yet again different aspects of regulatory logic evolve differently (Barrière and Ruvinsky 2014). Our work repeatedly uncovered common rules of functional evolution of transcriptional regulation. It further suggested that sequence conservation does not reliably predict functionally important elements, justifying continued search for more reliable predictors of functional conservation.

Reproductive performance under stress

To ensure long-term reproductive success organisms have evolved ways to mitigate the uncertainty of harsh environmental extremes. We seek to discover the strategies worms use to maintain reproductive capacity and as we wish understand their ecological and evolutionary significance.

We study reproduction under chronic heat stress, i.e. prolonged exposure to elevated temperatures that are lower than the classical heat shock. Surprisingly little is known about chronic stress, considering how often organisms encounter it in nature. With our Northwestern colleagues we constructed a simple mathematical model that yielded quantitatively accurate predictions of reproductive performance under a range of physiologically relevant conditions. This was verified by detailed time-resolved data (~100,000 embryos), obtained using newly developed experimental paradigms. We found that dynamic behavior of the reproductive system is determined by a small number of key components (McMullen et al. 2012), which we are now investigating.

All organisms have to determine whether given conditions are suitable for reproduction. When faced with intense heat, which dooms offspring survival, some, but not all worms cease reproduction. Why do others continue to lay eggs that will surely die? We identified the mechanistic cause of stoppage (cessation of ovulation) and found that, while protective, it has an inherent cost— a refractory period that delays the emergence of post-stress offspring. We showed that this creates a balanced trade-off under stress— continued reproduction at the cost of higher damage vs. preservation of reproductive capacity at the cost of temporal delay (Aprison and Ruvinsky 2014). We expect our work to reveal the molecular mechanisms by which environmental, physiological and cellular inputs are being integrated into fitness-determining decisions.

Evolution of nested gene arrangements

Many genes in complex eukaryotic genomes are contained within introns of other genes. In C. elegans only ~2.5% of protein-coding genes are so nested, whereas nearly 50% of non-protein-coding RNA genes are found in introns. Comparing these arrangements between species simplifies the inference of orthology and, therefore, of evolutionary fates of nested genes. We found that some genes form large families, which have persisted since before the common ancestor of Metazoa, while individual genes die relatively rapidly. Other genes exist mostly in single-copies, but turn over at a relatively slow rate. Observing similar patterns in other genomes suggests that a relationship between family size and the rate of gene turnover may be a universal feature of evolution (Wang and Ruvinsky, 2012). In addition, we developed a rules-and-Bayesian classifier that allows accurate predictions of previously undetected snoRNAs based on the properties of their host genes (Wang and Ruvinsky, 2010). Similar approaches could aid computational discovery of other types of rapidly evolving genes that are recalcitrant to discovery via conventional homology-based methods.

Heterozygosity in whole-genome shotgun assemblies

In collaboration with Eric Haag's group, we demonstrated that substantial fractions of genes in the genome assemblies of C. remanei, C. brenneri, and C. japonica are represented by two alleles (Barrière et al., 2009). This finding has significant implications for comparative genome analysis. For example, we showed that in these three genomes most pairs of closely related sequences (these could be interpreted as recently arisen paralogs) are in fact alleles. This suggests that gene complements are quite similar between all five currently sequenced Caenorhabditis species and offers an improved annotation of the whole-genome assemblies.

(c) The University of Chicago, 2009. Designed and maintained by Paul Wang