Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks

Intraspecific gene regulation in cis- and trans

Changes in gene expression underlie much of evolution and occur via either cis-acting mutations, which lie near the affected gene and act in a context-specific manner, or trans-acting mutations, which may be far from the affected gene and act through diffusible molecules such as transcription factors. A commonly held view is that most expression variation within species is controlled in trans- while expression differences between species are largely controlled in cis-. Here, we summarize recent intraspecific gene regulation studies and find, contrary to this widely held view, that many studies in diverse taxa have revealed a large role for cis-acting mutations underlying expression variation within species. A review of the existing literature also shows that preparations using whole organisms rather than individual tissues may be biased toward identifying trans-regulation. Moreover, we note several examples of predominantly cis-acting regulation in recently diverged populations adapted to different environments. We highlight the challenges of drawing general conclusions from comparisons among studies that use different methodologies and we offer suggestions for studies that will address outstanding questions concerning the evolution of gene regulation.

Gene-by-environment Interactions and Adaptive Body Size Variation in Mice From the Americas

The relationship between genotype and phenotype is often mediated by the environment. Moreover, gene-by-environment (GxE) interactions can contribute to variation in phenotypes and fitness. In the last 500 yr, house mice have invaded the Americas. Despite their short residence time, there is evidence of rapid climate adaptation, including shifts in body size and aspects of metabolism with latitude. Previous selection scans have identified candidate genes for metabolic adaptation. However, environmental variation in diet as well as GxE interactions likely impact body mass variation in wild populations. Here, we investigated the role of the environment and GxE interactions in shaping adaptive phenotypic variation. Using new locally adapted inbred strains from North and South America, we evaluated response to a high-fat diet, finding that sex, strain, diet, and the interaction between strain and diet contributed significantly to variation in body size. We also found that the transcriptional response to diet is largely strain-specific, indicating that GxE interactions affecting gene expression are pervasive. Next, we used crosses between strains from contrasting climates to characterize gene expression regulatory divergence on a standard diet and on a high-fat diet. We found that gene regulatory divergence is often condition-specific, particularly for trans-acting changes. Finally, we found evidence for lineage-specific selection on cis-regulatory variation involved in diverse processes, including lipid metabolism. Overlap with scans for selection identified candidate genes for environmental adaptation with diet-specific effects. Together, our results underscore the importance of environmental variation and GxE interactions in shaping adaptive variation in complex traits.

Predicting gene expression responses to environment in Arabidopsis thaliana using natural variation in DNA sequence

The evolution of gene expression responses is a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for cis regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying cis-regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. We first tested for evidence that cis regulation plays a role in environmental response, finding 14 and 15 motifs that were significantly enriched within the up- and down-stream regions of cold-responsive differentially regulated genes (DEGs). We next applied convolutional neural networks (CNNs), which learn de novo cis-regulatory motifs in DNA sequences to predict expression response to environment. We found that CNNs predicted differential expression with moderate accuracy, with evidence that predictions were hindered by biological complexity of regulation and the large potential regulatory code. Overall, approaches to predict DEGs between specific environments based only on proximate DNA sequences require further development, and additional information may be required.

Genotype-by-Environment Effects of Cis-Variations in the Atgl Promoter Mediate the Divergent Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species

Phenotypic plasticity plays an essential role in adaptive evolution. However, the molecular mechanisms of how genotype-by-environment interaction (G × E) effects shape phenotypic plasticity in marine organisms remain poorly understood. The crucial temperature-responsive trait triacylglycerol (TAG) content and its major gene adipose triglyceride lipase (Atgl) expression have divergent plastic patterns in two congeneric oyster species (Crassostrea gigas and Crassostrea angulata) to adapt to relative-cold/northern and relative-warm/southern habitats, respectively. In this study, eight putative loci were identified in the Atgl promoter region (cis-variations) between wild C. gigas and C. angulata that exhibited differential environmental responsiveness (G × E). The G and G × E effects of each locus were further dissected by measuring the Atgl gene expression of different genotypes in response to temperature changes at the cellular and organismal levels. Two transcription factors, non-environmentally responsive non-POU domain-containing octamer-binding protein (Nono) and environmentally responsive heterogeneous nuclear ribonucleoprotein K (Hnrnpk), were screened for binding to g.-1804 (G locus) and g.-1919 (G + G × E locus), respectively. The specificity of Nono binding to the C. angulata allele mediated the G effects of g.-1804, and the lower environmental sensitivity of Hnrnpk in C. angulata mediated the G × E effects of g.-1919, jointly regulating the trade-offs between higher constitutive and lower plastic expression of Atgl gene expression in C. angulata. This study served as an experimental case to reveal how the genetic variations with G and (or) G × E effects propagate into the divergent pattern of plasticity in environmental adaptive traits, which provides new insights into predicting the adaptability of marine organisms to future climate changes.

Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes

A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.

Stem cell transcriptional profiles from mouse subspecies reveal cis -regulatory evolution at translation genes

A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis -regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.

Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish

BACKGROUND

Cis-regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in non-coding regions is challenging, we have fewer examples of identified causative cis-regulatory mutations that underlie naturally occurring phenotypic variations than of causative amino acid-altering mutations. Because cis-regulatory elements have epigenetic marks of specific histone modifications, we can detect cis-regulatory elements by mapping and analyzing them. Here, we investigated histone modifications and chromatin accessibility with cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin-sequencing (ATAC-seq).

RESULTS

Using the threespine stickleback (Gasterosteus aculeatus) as a model, we confirmed that the genes for which nearby regions showed active marks, such as H3K4me1, H3K4me3, and high chromatin accessibility, were highly expressed. In contrast, the expression levels of genes for which nearby regions showed repressive marks, such as H3K27me3, were reduced, suggesting that our chromatin analysis protocols overall worked well. Genomic regions with peaks of histone modifications showed higher nucleotide diversity within and between populations. By comparing gene expression in the gills of the marine and stream ecotypes, we identified several insertions and deletions (indels) with transposable element fragments in the candidate cis-regulatory regions.

CONCLUSIONS

Thus, mapping and analyzing histone modifications can help identify cis-regulatory elements and accelerate the identification of causative mutations in the non-coding regions underlying naturally occurring phenotypic variations.

Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

Most vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here, we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in the direction predicted by a hair regeneration model: Wnt10a and Grem2a increased tooth replacement rate, whereas Bmp6 and Dkk2 strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA sequencing of stickleback dental tissue showed that Bmp6 overexpression resulted in an upregulation of Wnt inhibitors. Together, these data support a model in which different epithelial organs, such as teeth and hair, share genetic circuitry driving organ regeneration.