Genome Evolution: How Sister Genes Grow Apart

Evolution of binding preferences among whole-genome duplicated transcription factors

Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge was studied in a few cases only. To provide a genome-scale view, we considered the set of budding yeast TFs classified as whole-genome duplication (WGD)-retained paralogs (~35% of all specific TFs). Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA-binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed uneven splitting of ancestral preferences between duplicates, and the preferential acquiring of new targets by the least conserved paralog (biased neo/sub-functionalization). Interactions between paralogs were rare, and, when present, occurred through weak competition for DNA-binding or dependency between dimer-forming paralogs. We discuss the implications of our findings for the evolutionary design of transcriptional networks.

Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes

The large spectrum of hearing sensitivity observed in primates results from the impact of environmental and behavioral pressures to optimize sound perception and localization. Although evidence of positive selection in auditory genes has been detected in mammals including in Hominoids, selection has never been investigated in other primates. We analyzed 123 genes highly expressed in the inner ear of 27 primate species and tested to what extent positive selection may have shaped these genes in the order Primates tree. We combined both site and branch-site tests to obtain a comprehensive picture of the positively selected genes (PSGs) involved in hearing sensitivity, and drew a detailed description of the most affected branches in the tree. We chose a conservative approach, and thus focused on confounding factors potentially affecting PSG signals (alignment, GC-biased gene conversion, duplications, heterogeneous sequencing qualities). Using site tests, we showed that around 12% of these genes are PSGs, an α selection value consistent with average human genome estimates (10-15%). Using branch-site tests, we showed that the primate tree is heterogeneously affected by positive selection, with the black snub-nosed monkey, the bushbaby, and the orangutan, being the most impacted branches. A large proportion of these genes is inclined to shape hair cells and stereocilia, which are involved in the mechanotransduction process, known to influence frequency perception. Adaptive selection, and more specifically recurrent adaptive evolution, could have acted in parallel on a set of genes (ADGRV1, USH2A, PCDH15, PTPRQ, and ATP8A2) involved in stereocilia growth and the whole complex of bundle links connecting them, in species across different habitats, including high altitude and nocturnal environments.

How Transcription Networks Evolve and Produce Biological Novelty

The rewiring of gene regulatory networks over evolutionary timescales produces changes in the patterns of gene expression and is a major source of diversity among species. Yet the molecular mechanisms underlying evolutionary rewiring are only beginning to be understood. Here, we discuss recent analyses in ascomycete yeasts that have revealed several general principles of network rewiring. Specifically, we discuss how transcription networks can maintain a functional output despite changes in mechanism, how specific types of constraints alter available evolutionary trajectories, and how regulatory rewiring can ultimately lead to phenotypic novelty. We also argue that the structure and "logic" of extant gene regulatory networks can largely be accounted for by constraints that shape their evolutionary trajectories.

Reshuffling transcriptional circuits: how microorganisms adapt to colonize the human body

Several hundred taxa of microorganisms-including bacteria, archaea and eukaryotes-inhabit the human body. What did it take for these species to become stable residents of humans? Recent reports illustrate how evolutionary changes in transcriptional circuits played a pivotal role in the adaptation of single-celled eukaryotes to colonize mammals.