Camille Berthelot

The immune system plays key roles in the mammalian uterine cycle, particularly for menstruation, a dramatic tissue renewal mechanism independently acquired four times in eutherians. These roles specifically involve natural killer (NK) cells through the expression of surface killer cell immunoglobulin-like receptors (KIRs) and killer cell lectin-like receptors (KLRs), respectively part of the immunoglobulin-like and lectin-like gene superfamilies with poorly resolved phylogenetic histories. Acquisition of menstruation in primates seemingly coincides with a large expansion of the KIR family, suggesting that innovations in NK cell receptor families may have been crucial for the evolution of menstruation. To test this hypothesis, we performed an in-depth analysis of the evolutionary histories of the KIR and KLR gene families across 41 mammalian genomes, including all four clades that acquired menstruation. Our results reveal the existence of undescribed KIR and KLR genes across many mammalian species, including elephants, armadillos, rhinoceroses, and leaf-nosed bats, as well as a novel subfamily within the KLR phylogeny. Altogether, we identify more than twice as many NK cell receptor genes across mammals than currently reported in reference genomes. Further, we show that the KIR gene family has experienced intensified purifying selection in menstruating species compared with non-menstruating species, suggesting specific evolutionary pressures related to menstruation and illustrating gene-level convergence linked to the phenotype. Our data, however, do not support that menstruation coincides with expansions or contractions in NK cell receptor repertoires, except in primates, highlighting both shared and lineage-specific immune adaptations to rapidly evolving reproductive biology.

Whole genome duplication (WGD) events during early vertebrate evolution may have promoted phenotypic innovation by expanding the genetic material for functional diversification. However, their ancient origins obscure how gene regulation evolved during rediploidization, the process that generates duplicate genes and regulatory elements following WGD. Salmonids provide a unique window to these mechanisms, because they experienced a more recent autotetraploid WGD and remain at an earlier stage of rediploidization. Here we generated 771 multiomics datasets spanning embryonic and adult tissues in Atlantic salmon and rainbow trout to investigate the evolution of gene expression and regulatory elements. Our analyses show that regulatory evolution following the salmonid WGD was shaped by developmental and tissue-specific constraints known to act across vertebrate species. We identify a peak of within-genome regulatory constraint at the vertebrate phylotypic period, associated with the functional retention of duplicated enhancer pairs harbouring deeply conserved non-coding elements enriched in motifs for master developmental transcription factors. We further identify roles for enhancers and transposable elements in the expression divergence of duplicated genes. This study advances the understanding of regulatory evolution following WGD and offers an open resource supporting vertebrate comparative genomics and research applications in salmonid aquaculture and conservation.

Background: Changes in gene expression regulation are central to the acquisition of novel phenotypes during mammalian evolution. However, transcriptomes substantially accumulate neutral divergence over evolutionary time. As a result, selection-driven gene expression shifts are difficult to distinguish from neutral changes, thereby blurring adaptive signatures during genome evolution. Here, we integrate comparative multiomics data within a phylogeny-aware framework of quantitative trait evolution to jointly investigate how gene expression and regulation have evolved in African mole-rats. This group of rodents displays striking physiological adaptations to subterranean life; how those adaptations are encoded in their genomes remains poorly characterised. Results: Using RNA-seq from liver and heart in two mole-rat species and two rodent outgroups, we reliably identify hundreds of genes whose expression levels have experienced lineage-specific accelerated evolution consistent with selection rather than drift. To connect expression evolution with regulatory mechanisms, we integrate this transcriptome data with epigenomic profiles of cis-regulatory landscapes, which experience high turnover in mammalian evolution. Conclusions: Our results demonstrate that genes with lineage-specific expression shifts are surrounded by epigenomic landscapes that also display signals of accelerated evolution, providing support for selection over genomic processes diverging at different rates. Our approach illuminates how gene regulation and expression evolve in concert in this mammalian model and highlights genomic loci with concordant evidence for phenotypic adaptation. The molecular signatures we observe reveal selective pressures acting on key pathways for mole-rat physiology, including metabolism and stress responses.

Endometriosis is a common complex gynecological condition that is difficult to efficiently diagnose and remains poorly understood. Menstrual fluid provides

Changes in gene regulation largely contribute to differences in cellular identities and phenotypes between species. Single-nucleus assays for transposase-accessible chromatin with sequencing (snATAC-seq) are an efficient strategy to identify putative gene regulatory elements and provide new insight into evolutionary divergence of regulatory programmes. However, no dedicated framework exists to integrate and compare snATAC-seq data across species, while methods designed for single-cell gene expression data have serious limitations. Here we present sPYce, a cross-species snATAC-seq integration method that relies on sequence composition similarities through k-mer histograms of regulatory regions, removing the need for genome alignments to anchor data from different species. sPYce can embed datasets from multiple species into the same mathematical space and permits further downstream analysis steps. We benchmarked sPYce against existing approaches on two publicly available datasets spanning more than 160 myr of evolution, showing that it successfully uncovers conserved cellular programmes while preserving biologically relevant species-specific differences. By comparing cerebellar development in mice and opossums, sPYce identifies regulatory divergence in granule cell differentiation programmes, particularly driven by nuclear factor 1. As an easy-to-use, alignment-free cross-species snATAC-seq integration approach, sPYce opens new perspectives to compare gene regulatory evolution across species.

Les phénomènes évolutifs qui perturbent l’organisation des gènes dans les génomes eucaryotes sont de deux types : les changements dans l’ordre des gènes, ou réarrangements, et les modifications du contenu en gènes du génome, par duplications, délétions ou gains de gènes. Ces processus sont mal connus, tant au niveau de leurs mécanismes d’apparition que de leur impact fonctionnel et sélectif. Ce travail de thèse s’articule autour de deux projets. Le premier s’intéresse à la distribution des points de cassure de réarrangements évolutifs entre un génome ancestral et ses descendants modernes. Cette distribution a été modélisée en fonction des caractéristiques locales du génome pour mettre en évidence quels facteurs influencent la probabilité de cassure. Nos résultats montrent que la distribution des cassures peut s’expliquer simplement comme une fonction de la longueur des espaces intergéniques, fonction qui est cependant non-linéaire contrairement aux attentes sous un régime aléatoire classique. La répartition des points de cassure dans les génomes semble principalement liée à des propriétés de structure, et n’est que peu soumise à des contraintes de sélection. Elle pourrait être liée à la structure chromatinienne du génome. Le second projet s’inscrit dans le cadre du séquençage du génome du poisson zèbre, et fournit un aperçu global de l’organisation de ce génome. Les génomes de poissons téléostéens sont anciennement dupliqués : l’analyse est axée sur les conséquences de cette duplication. Les résultats montrent que le génome du poisson zèbre présente une organisation assez typique d’un génome téléostéen. Les gènes retenus en deux copies après la duplication du génome appartiennent à des catégories fonctionnelles particulières, et sont biaisés vers des gènes déjà conservés après les duplications 1R et 2R ayant eu lieu au début de l’histoire des vertébrés.

Uterine disorders and menstrual abnormalities are prevalent reproductive conditions with significant clinical consequences. Recent genome-wide association studies have identified hundreds of variants contributing to different uterine disorders, while epidemiological evidence suggests that these disorders co-occur more frequently than expected, implying shared genetic mechanisms. However, the specific genetic variants and biological pathways underlying this shared architecture remain poorly characterized. Here, we conducted a uterus-centric, multi-trait genome-wide association analysis across ten uterine disorders in a European cohort to elucidate this shared genetic architecture. Further, we embedded this architecture in a functional and population genomics framework to investigate its plausible biological mechanisms and its evolutionary history in humans. We confirm strong positive genetic correlations between major uterine disorders and identify 31 independent susceptibility loci jointly affecting the genetic risk of multiple uterine pathologies, substantiating an intertwined biological basis. Populational analyses demonstrated that several of these susceptibility variants exhibit pronounced allele frequency differentiation across global populations suggestive of recent polygenic selection, including variants with well-supported regulatory functions at the ESR1-CCDC170 , WNT4 , SFR1, FOXO1, ITPR1, DMRT1 and CDKN2B loci. Notably, we show that most derived alleles acquired during recent human evolution increase risk across multiple uterine disorders and may evolve under antagonistic selection. These findings provide functional annotation and population-level prioritization of genetic variants influencing multiple uterine disorders. They also highlight how past evolutionary histories may contribute to population differences in uterine disease prevalence and pathogenesis.

The immune system plays key roles in the mammalian uterine cycle, particularly for menstruation, a dramatic tissue renewal mechanism independently acquired four times in eutherians. These roles specifically involve NK cells through the expression of KIR and KLR surface receptors, respectively part of the immunoglobulin-like and lectin-like gene superfamilies with poorly resolved phylogenetic histories. Acquisition of menstruation in primates reportedly coincides with a large expansion of the KIR family, suggesting that gains and losses in NK cell receptor families may have been crucial for the evolution of menstruation. To test this hypothesis, we performed an in-depth analysis of the evolutionary histories of the KIR and KLR gene families across 41 mammalian genomes, including all four clades that acquired menstruation. Our results reveal the existence of undescribed KIR and KLR genes across many mammalian species, including elephants, armadillos, rhinoceroses, and leaf-nosed bats, as well as a novel subfamily within the KLR phylogeny. Altogether, we identify more than twice as many NK cell receptor genes across mammals than currently reported in reference genomes. Further, we show that the KIR gene family has experienced intensified selection in menstruating species compared non-menstruating species, suggesting specific evolutionary pressures related to menstruation. Our data however do not support that menstruation coincides with expansions or contractions in NK cell receptor repertoires, even in primates, invalidating a current hypothesis regarding how menstruation evolved.

Early vertebrate autotetraploidization events may have enabled major innovations by expanding the genetic material for functional diversification, yet their ancient timing obscures how genome doubling reshaped gene regulatory evolution. Salmonids provide a unique window to these mechanisms, because they experienced a comparatively recent autotetraploidization and are earlier in the rediploidization process - which creates new genes and regulatory elements during evolution. Here, using large-scale multiomics spanning embryonic and adult tissues in two salmonids, we investigate gene regulatory evolution following genome doubling and rediploidization, which we show is governed by developmental and tissue-specific context, with a period of maximal constraint at advanced stages of embryogenesis. This work advances understanding of vertebrate genome evolution, while providing an open resource supporting salmonid aquaculture and conservation.