Meiotic recombination evolution : Prdm9 gene variation and evolution in mice

Évolution de la recombinaison méiotique: variation et fonction du gène Prdm9 chez la souris. L’espèce M. musculus est divisée en trois sous-espèces dont deux en Europe, M. m. musculus et M. m. domesticus. Lorsque certaines lignées de souris venant de ces différentes sous-espèces (PWD de M. m. musculus et C57BL/6 de M. m. domesticus) sont croisées, on observe une stérilité chez les descendants mâles, due à un arrêt en prophase de la première division de méiose. Cette stérilité est liée à des incompatibilités génétiques qui impliquent une combinaison spécifique d’allèles du gène Prdm9, une hétérozygotie génomique ainsi qu’une région du chromosome X. Le gène Prdm9, qui est l’un des gènes évoluant le plus rapidement chez les rongeurs et les primates, a ainsi été proposé être un gène impliqué dans la spéciation. Au niveau moléculaire, Prdm9 spécifie la localisation des événements de recombinaison méiotique en des sites qui peuvent différer selon les allèles. Lors de ma thèse, j’ai entrepris de tester l’hypothèse du rôle de Prdm9 dans la spéciation en évaluant la généralité des incompatibilités dues à Prdm9. J’ai testé la fertilité de 32 croisements réalisés à partir de 8 lignées de souris issues de la nature, 4 de chaque sous espèce et portant des allèles de Prdm9 distincts. L’analyse du poids testiculaire et de la spermatogénèse par histologie et immuno-cytochimie a révélé un phénotype sauvage chez tous ces hybrides. Par contre, en croisant la lignée C57BL/6 avec les 4 lignées de M. m. musculus utilisées précédemment, j’ai observé une corrélation entre la présence d’un allèle spécifique de M. m. musculus (PWD) et la stérilité, avec des variations des phénotypes indiquant que les facteurs impliqués n’ont pas été fixés.J’ai donc démontré que la stérilité hybride est restreinte à des combinaisons spécifiques d’allèles Prdm9 et de fonds génétiques, ce qui définit de manière précise le contexte dans lequel Prdm9 pourrait jouer un rôle dans la spéciation. Compte tenu du phénomène d’érosion des sites de PRDM9 par conversion génique et que leur hétérozygotie peut conduire à des défauts de recombinaison et à la stérilité, mes données conduisent également à des prédictions sur la fréquence et l’activité de différents allèles de Prdm9 sur les génomes de M. m. musculus et M. m. domesticus.En parallèle, j’ai également initié une étude portant sur 300 souris sauvages d’origines géographiques et phylogénétiques variées : par capture et séquençage de régions génomiques d’intérêt, nous chercherons à déchiffrer les modes de sélection régissant l’évolution de la région génomique du gène Prdm9. Lors de ma thèse, j’ai entrepris de tester l’hypothèse du rôle de Prdm9 dans la spéciation en évaluant la généralité des incompatibilités dues à Prdm9. J’ai testé la fertilité de 32 croisements réalisés à partir de 8 lignées de souris issues de la nature, 4 de chaque sous espèce et portant des allèles de Prdm9 distincts. L’analyse du poids testiculaire et de la spermatogénèse par histologie et immuno-cytochimie a révélé un phénotype sauvage chez tous ces hybrides. Par contre, en croisant la lignée C57BL/6 avec les 4 lignées de M. m. musculus utilisées précédemment, j’ai observé une corrélation entre la présence d’un allèle spécifique de M. m. musculus (PWD) et la stérilité, avec des variations des phénotypes indiquant que les facteurs impliqués n’ont pas été fixés.J’ai donc démontré que la stérilité hybride est restreinte à des combinaisons spécifiques d’allèles Prdm9 et de fonds génétiques, ce qui définit de manière précise le contexte dans lequel Prdm9 pourrait jouer un rôle dans la spéciation. Compte tenu du phénomène d’érosion des sites de PRDM9 par conversion génique et que leur hétérozygotie peut conduire à des défauts de recombinaison et à la stérilité, mes données conduisent également à des prédictions sur la fréquence et l’activité de différents allèles de Prdm9 sur les génomes de M. m. musculus et M. m. domesticus.Meiotic recombination evolution: Prdm9 gene variation and evolution in miceHouse mouse Mus musculus is divided into three sub species, two of which are found in Europe, M. m. musculus and M. m. domesticus. Male hybrids from some mouse strains derived from these sub-species (PWD from M. m. musculus and C57BL/6 from M. m. domesticus) are sterile with a meiotic arrest during the first meiotic prophase. This sterility is due to genetic incompatibilities involving heterozygosity at Prdm9 and in the genome as well as a locus on the X chromosome. Prdm9, which one of the fastest evolving gene in primates and rodents, was thus proposed to be a speciation gene. At the molecular level, Prdm9 is known to specify the sites of meiotic recombination which can be distinct in different Prdm9 alleles.During my thesis, I tested the hypothesis of the role of Prdm9 in speciation by evaluating the generality of incompatibilities due to Prdm9. I tested the fertility of 32 hybrids made by crossing 8 wild-derived mouse strains from both sub-species and carrying distinct Prdm9 alleles. Based on the analysis of testis weight and of spermatogenesis by histological and cytological analysis, I observed a wild type phenotype in all hybrids. Instead when C57BL/6 was crossed with the four M. m. musculus strains used in previous crosses, I observed a correlation between the presence of the PWD allele and sterility, with variations in the strength of the phenotype.I have thus shown that hybrid sterility is limited to specific combinations of Prdm9 alleles together with specific genomic backgrounds which define contexts in which Prdm9 could act as a speciation gene. Given that PRDM9 sites are eroded by gene conversion and that heterozygosity at PRDM9 sites can lead to defects in meiotic recombination and to sterility, my observations lead to predictions about Prdm9 allele frequencies and Prdm9 historical activities on the genomes of M. m. musculus and M. m. domesticus.Simultaneously, I initiated a study on nearly 300 mice of various geographic and phylogenetic origins: using genomic sequence capture technology, we are aiming to decipher selection forces affecting the evolution of Prdm9 gene genomic region

Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite

International audienceIn humans and mice, meiotic recombination events cluster into narrow hotspots whose genomic positions are defined by the PRDM9 protein via its DNA binding domain constituted of an array of zinc fingers (ZnFs). High polymorphism and rapid divergence of the Prdm9 gene ZnF domain appear to involve positive selection at DNA-recognition amino-acid positions, but the nature of the underlying evolutionary pressures remains a puzzle. Here we explore the variability of the Prdm9 ZnF array in wild mice, and uncovered a high allelic diversity of both ZnF copy number and identity with the caracterization of 113 alleles. We analyze features of the diversity of ZnF identity which is mostly due to non-synonymous changes at codons −1, 3 and 6 of each ZnF, corresponding to amino-acids involved in DNA binding. Using methods adapted to the minisatellite structure of the ZnF array, we infer a phylogenetic tree of these alleles. We find the sister species Mus spicilegus and M. macedonicus as well as the three house mouse (Mus musculus) subspecies to be polyphyletic. However some sublineages have expanded independently in Mus musculus musculus and M. m. domesticus, the latter further showing phylogeographic substructure. Compared to random genomic regions and non-coding minisatellites, none of these patterns appears exceptional. In silico prediction of DNA binding sites for each allele, overlap of their alignments to the genome and relative coverage of the different families of interspersed repeated elements suggest a large diversity between PRDM9 variants with a potential for highly divergent distributions of recombination events in the genome with little correlation to evolutionary distance. By compiling PRDM9 ZnF protein sequences in Primates, Muridae and Equids, we find different diversity patterns among the three amino-acids most critical for the DNA-recognition function, suggesting different diversification timescales

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat

Abstract Background The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key strains. Comparison of genomic variation between two closely related rat strains with different phenotypes has been proposed as an effective strategy for the discovery of candidate strain-specific regions involved in phenotypic differences. We developed a method to prioritise strain-specific haplotypes by integrating genomic variation and genomic regulatory data predicted to be involved in specific phenotypes. Specifically, we aimed to identify genomic regions associated with Metabolic Syndrome (MetS), a disorder of energy utilization and storage affecting several organ systems. Results We compared two Lyon rat strains, Lyon Hypertensive (LH) which is susceptible to MetS, and Lyon Low pressure (LL), which is susceptible to obesity as an intermediate MetS phenotype, with a third strain (Lyon Normotensive, LN) that is resistant to both MetS and obesity. Applying a novel metric, we ranked the identified strain-specific haplotypes using evolutionary conservation of the occupancy three liver-specific transcription factors (HNF4A, CEBPA, and FOXA1) in five rodents including rat. Consideration of regulatory information effectively identified regions with liver-associated genes and rat orthologues of human GWAS variants related to obesity and metabolic traits. We attempted to find possible causative variants and compared them with the candidate genes proposed by previous studies. In strain-specific regions with conserved regulation, we found a significant enrichment for published evidence to obesity—one of the metabolic symptoms shown by the Lyon strains—amongst the genes assigned to promoters with strain-specific variation. Conclusions Our results show that the use of functional regulatory conservation is a potentially effective approach to select strain-specific genomic regions associated with phenotypic differences among Lyon rats and could be extended to other systems

Habitat partitioning of soil microbial communities along an elevation gradient: from plant root to landscape scale

International audienceWithin a landscape, multiple habitats exist for soil microbial communities. But how these habitats shape community composition requires an understanding of the way in which microbial diversity is impacted across a broad range of spatial scales. Mountain ecosystems are excellent systems to study microbial communities, because a multitude of climate and soil variables change within a relatively small distance. We investigated microbial community structure in bulk and rhizosphere soils beneath three plant species, Vaccinium myrtillus, Juniperus communis and Picea abies, that structure local plant communities along an elevation gradient in the French Alps. We examined the impact that climate, soil properties, plant diversity and plant root chemical and morphological traits had on microbial αand β-diversities. The most abundant bacterial phyla detected in both bulk and rhizosphere soils were Proteobacteria, Actinobacteria, Acidobacteria and Verrucomicrobia. Along the elevation gradient, bacterial phyla did not display a clear distribution pattern between bulk and rhizosphere soils. For fungi, dominant phyla were Ascomycota and Basidiomycota, and contrasting distribution patterns were found between bulk and rhizosphere soils. Overall, bacterial and fungal α-diversity responded differently to elevation as well to soil compartments (bulk versus rhizosphere soil), revealing no significant patterns in bulk soil beneath any of the structuring plant species, but increasing in the rhizosphere compartment of P. abies just below the treeline. Changes in bacterial β-diversity with elevation were related mostly to soil physical and chemical properties. Bacterial and fungal α-diversity in rhizosphere communities were more related to plant species identity, vegetation diversity and belowground plant traits compared to soil properties, whilst the opposite was found for bulk soil. Our results highlight that environmental changes at the landscape scale (e.g. associated to elevation, soil properties or climate), impact significantly soil microbial communities, but vegetation refines communities at a local scale via the rhizosphere niche

Additional file 3: of Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat

All relevant characteristics of genes that are overlapping HVRs with conserved TFBS from all three factors and have SSVs in promoters that can be one-to-one associated with genes in at least one strain comparison. (XLSX 70 kb

Geographic distribution of groups of alleles in the house mouse.

<p>The shape of the symbols indicates subspecies (square, <i>M. m. domesticus</i>, circles <i>M. m. musculus</i>, triangles <i>M. m. castaneus</i>). Colors indicate lineages as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g003" target="_blank">Fig. 3</a>.</p

Predicted DNA binding sites of mouse <i>Prdm9</i> ZnF alleles and dispersed repeats.

<p>(A) Distribution among <i>Prdm9</i> alleles of the proportion of the coverage of hits of the predicted recognized DNA motifs that fall in dispersed repeated sequences, as annotated on the reference mouse genome. (B) Absolute proportion of hit coverage falling in a given repeat family for each of the sequenced allele. Red cross: expected proportion if hit coverage was proportional to the coverage of the family in the genome. Red circles: median, first and third quartile of the distribution across alleles. Note the log scales. (C) Projection of the alleles on the first two axes of the Principal Component Analysis on the relative proportion of hits of each allele in the different repeated families. Symbol colors refer to lineage colors as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g002" target="_blank">Fig. 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g003" target="_blank">3</a>. Symbol shapes are arbitrary. PC1 absorbs 35% of the variance, and PC2 13%.</p

Simplified triplet protein variants of the <i>Prdm9</i> ZnF array in wild mice.

<p>Sequence identifiers are highlighted with colors as in the phylogenetic tree of DNA alleles in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g002" target="_blank">Fig. 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g003" target="_blank">3</a>. Alleles of laboratory strains previously sequenced are identified as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Parvanov1" target="_blank">[12]</a>. Each ZnF is simplified to the three most variable codons −1, 3 and 6, and separated with a dash from the next ZnF. Sequences start at the first functional C2H2 ZnF (the second repeat) and end at the last carboxy-terminal ZnF of the protein. A few remarkable stretches of zinc fingers are highlighted: some are shared between most <i>M. musculus</i> protein variants (QNK-QDQ, red), some are shared between the twin species <i>spicilegus</i> and <i>macedonicus</i> (QNQ-ANK-**Q-QDQ, purple), some are shared between <i>castaneus</i> and <i>musculus</i> alleles (ANQ-ESK, yellow) and some others are specific or enriched in each of <i>domesticus</i> (QHQ-QDK, dark blue; AVQ-AVQ, light blue), <i>castaneus</i> (VVQ, green), <i>M. spretus</i> (ADK-VNQ; QNQ-ADK, grey); <i>M. macedonicus</i> (QHK-QNQ, purple) and <i>M. spicilegus</i> (QNQ-ADK, grey) groups of alleles.</p

Repeat copy number variability of <i>Mus</i> ZnF <i>Prdm9</i> and size heterozygosity.

<p>N: number of mice. NA: number of allele sizes. H: observed heterozygosity, He: Expected heterozygosity in panmictic population based on allele frequencies.</p

Inferred phylogeny of the <i>Prdm9</i> ZnF domain alleles.

<p>Taxon names on the branches include allele number, followed by the number of observations, then by taxon code (abbreviation of species name), country code, locality name and number of ZnF repeats. Numbers at the nodes indicate the level of confidence of the node (only values >0.5 reported).</p