bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.07.03.450995

Promoter architecture links gene duplication with transcriptional divergence

Hagai, T.·Fraimovitch, E.
View original source ↗Export metadata ↓

Abstract

Gene duplication is thought to be a central mechanism in evolution to gain new functions, but gene families vary greatly in their rates of gene duplication and long-term retention. Here, we discover a link between the promoter architecture of vertebrate genes and their rate of duplication: Genes that harbor CpG Islands in their promoters (CGI genes) - nearly 60% of our genes - have rarely duplicated in recent evolutionary times, and most CGI gene duplication events predate the emergence of CGI as a major regulatory element of vertebrate genes. In contrast, CGI-less genes predominate duplications that have occurred since the divergence of vertebrates. Furthermore, CGI-less paralogs are transcriptionally more divergent than CGI paralogs, even when comparing CGI and CGI-less paralogs that have duplicated at similar evolutionary times - suggesting greater capacity of CGI-less promoters to enable divergence in expression. This higher divergence between CGI-less paralogs is also reflected in lower similarity of transcription factors that bind to the promoters of CGI-less paralog pairs in comparison with CGI paralogs. Finally, CGI-less paralogs have a greater tendency to sub- and neo-functionalize, and they transcriptionally diversify faster following duplication. Our results highlight the links between promoter architecture, gene expression plasticity and their impact on gene expansion, and unravel an unappreciated role of CGI elements in shaping genome evolution. Significance statementGene duplication generates extra gene copies, providing material for evolution of new functions. However, many duplicated genes are eliminated due to functional and regulatory constraints. The evolutionary processes that govern the elimination and persistence of duplicated genes are not well understood. Here, we focus on CpG Islands (CGIs) - important elements that occur in the majority of gene promoters. We show that genes with CGIs in their promoters have duplicated almost exclusively in ancient times, and nearly all recent duplications involve CGI-less genes. Furthermore, duplicated CGI-less genes diverge more in expression and display more distinctive transcription and cis-regulation compared to duplicated CGI-genes. Our results demonstrate how promoter structure influences transcriptional evolvability and, in turn, the retention of new genes.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hagai, T., Fraimovitch, E.. 2021-07-04. Promoter architecture links gene duplication with transcriptional divergence. https://doi.org/10.1101/2021.07.03.450995

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Measuring the strength of selection and pollen limitation on flower colour along an urban rural cline in Hesperis matronalis

Closely located urban and rural environments can differ in temperature, water availability, species diversity, and more. As a result, organisms in urban environments may experience different selection than those in rural environments. We investigated whether differences in selection might explain a previously identified urban-rural cline in the flower colour of Hesperis matronalis (dame's rocket). To explore whether plants in urban and rural environments are impacted by possible differences in pollinator availability or behavior, we performed a pollen supplementation experiment. We did not detect an effect of pollen supplementation on seed production in either setting (urban or rural), indicating that there is limited opportunity for any differences in pollinator availability or visitation to explain the cline in flower colour. We also measured the strength of selection acting on flower colour to investigate if it differed between urban and rural populations. In all but one population, we failed to detect significant linear or non-linear selection on flower colour, suggesting that selection on flower colour does not differ between urban and rural populations. Our results suggest that the urban-rural flower colour cline is likely not caused by differences in selection or pollen-limitation and may be due to stochastic forces.

evolutionary biology↗
bioRxiv2026

An elongated lifespan is associated with higher oxidative protection of flight tissue in Heliconiini butterflies

Evolutionary theories of ageing often invoke trade-offs in resource allocation between somatic maintenance and other important physiological functions. One proposed mechanistic mediator of these trade-offs is oxidative stress, which arises from an imbalance between an organism's production of reactive oxygen species and its ability to detoxify them. Accordingly, many long-lived species across the animal kingdom show evidence for resistance to oxidative stress. However, it can be difficult to associate lifespan differences with oxidative phenotypes when comparing species across wide taxonomic distances, which may also show large differences in physiology. Butterflies in the long-lived Heliconius genus show a 3-fold lifespan extension and slowed ageing in comparison with their close relatives in the Heliconiini tribe, to whom they are phylogenetically, ecologically, and physiologically similar. However, proximate explanations for this extended longevity are currently lacking. Here, we leverage the neat comparative framework between Heliconius hecale and Dryas iulia, a shorter-lived Heliconiini outgroup, to test whether the observed lifespan differences between the two species are associated with differences in oxidative physiology. Our findings suggest superior oxidative protection of thoracic tissue in the longer-lived H. hecale compared to D. iulia, as evidenced by increased superoxide dismutase activity, increased total antioxidant capacity, and a corresponding reduction in lipid peroxidation in this tissue. Considering the metabolic demands of insect flight, we suggest that this oxidative phenotype may contribute to the extended longevity of Heliconius by enhancing protection of thoracic tissues against oxidative damage, representing a plausible proximate pro-longevity mechanism in this genus.

evolutionary biology↗
bioRxiv2026

Both genetic and social inheritance influence female aggressive and submissive behavior in a wild primate

Agonistic interactions are important determinants of resource access in wild animals, but their genetic basis remains poorly understood. Here we use a quantitative genetics approach to estimate the heritability of aggressive and submissive behavior of wild female baboons, considering relative rates of both individual and dyadic aggression and submission. To control for the social inheritance that creates kin-based dominance hierarchies, we implemented a multi-matrix model that included a social status similarity matrix alongside the additive genetic matrix. Despite a substantial contribution of social inheritance, especially for submissive behavior, we found heritable components for both aggressive and submissive behavior (h2=0.21 and h2=0.09-0.11, respectively). In dyadic models, aggressive behavior was primarily influenced by the aggressor's genotype (a direct genetic effect), while submissive behavior was primarily affected by the social partner's genotype (an indirect genetic effect). Finally, we found evidence for a negative genetic (but not phenotypic) correlation between aggressive and submissive behavior within dyads, and a negative genetic correlation between submissive behavior and eliciting submissive behavior. Together, our results highlight how direct genetic, indirect genetic, and social inheritance effects combine to influence primate social behavior.

evolutionary biology↗