Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

International audienceReconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements , and protein divergence into a single evolutionary framework

Quantitative study of structural variations of chromosomes in saccharomyces cerevisiae

L’accumulation de remaniements de la structure des chromosomes aussi appelés variations structurelles (SV) est un important contributeur à la transformation des cellules malignes et à la constitution d’une hétérogénéité intratumorale. Nous avons développé un outil bio-informatique qui permet désormais d’obtenir une image fine de ces SV qui se produisent dans le génome humain. Nous avons ainsi pu démontrer l’existence de SV présentes à de faibles fréquences dans différentes populations cellulaires supposées clonales montrant que les taux de formation des SV pourraient être grandement sous-estimés. Parallèlement, nous avons montré que le niveau d’instabilité des individus dépend de facteurs génétiques de prédisposition. Pour les identifier, nous avons développé des systèmes génétiques de mesure des taux de SV chez la levure qui vont nous permettre d'identifier les gènes contrôlant l'instabilité chromosomique par analyse de liaison à grande échelle. Ces régulateurs représenteront de nouveaux gènes candidats impliqués dans le développement du cancer chez l’homme, car les déterminants génétiques impliqués dans le métabolisme de l'ADN sont très conservés entre la levure et les mammifères.The accumulation of chromosomal rearrangements also called Structural Variations (SV) is a major contributor to the transformation of tumoral cells and to the constitution of intratumoral heterogeneity. We have developed a bio-informatic tool that can now provide a sharp image of SV that occur in the human genome. We have demonstrated the existence of SV present in low proportions in different supposedly clonal cell populations showing that the rates of SV formation could be greatly underestimated. In parallel, we have shown that the level of instability of the genome depends on predisposition factors. To identify those, we have developed genetic assays to measure the rate of SV in yeast that will allow us to identify new genes controlling the stability of the genome using large scale linkage analysis. These regulators represent new gene-candidates involved in the development of cancer in human as the determinants involved in DNA metabolism are very conserved between yeast and mammals

Etude quantitative des variations structurelles des chromosomes chez Saccharomyces cerevisiae

The accumulation of chromosomal rearrangements also called Structural Variations (SV) is a major contributor to the transformation of tumoral cells and to the constitution of intratumoral heterogeneity. We have developed a bio-informatic tool that can now provide a sharp image of SV that occur in the human genome. We have demonstrated the existence of SV present in low proportions in different supposedly clonal cell populations showing that the rates of SV formation could be greatly underestimated. In parallel, we have shown that the level of instability of the genome depends on predisposition factors. To identify those, we have developed genetic assays to measure the rate of SV in yeast that will allow us to identify new genes controlling the stability of the genome using large scale linkage analysis. These regulators represent new gene-candidates involved in the development of cancer in human as the determinants involved in DNA metabolism are very conserved between yeast and mammals.L’accumulation de remaniements de la structure des chromosomes aussi appelés variations structurelles (SV) est un important contributeur à la transformation des cellules malignes et à la constitution d’une hétérogénéité intratumorale. Nous avons développé un outil bio-informatique qui permet désormais d’obtenir une image fine de ces SV qui se produisent dans le génome humain. Nous avons ainsi pu démontrer l’existence de SV présentes à de faibles fréquences dans différentes populations cellulaires supposées clonales montrant que les taux de formation des SV pourraient être grandement sous-estimés. Parallèlement, nous avons montré que le niveau d’instabilité des individus dépend de facteurs génétiques de prédisposition. Pour les identifier, nous avons développé des systèmes génétiques de mesure des taux de SV chez la levure qui vont nous permettre d'identifier les gènes contrôlant l'instabilité chromosomique par analyse de liaison à grande échelle. Ces régulateurs représenteront de nouveaux gènes candidats impliqués dans le développement du cancer chez l’homme, car les déterminants génétiques impliqués dans le métabolisme de l'ADN sont très conservés entre la levure et les mammifères

A set of genetically diverged Saccharomyces cerevisiae strains with markerless deletions of multiple auxotrophic genes

International audienceGenome analysis of over 70 Saccharomyces strains revealed the existence of five groups of genetically diverged S. cerevisiae wild-type isolates, which feature distinct genetic backgrounds and reflect the natural diversity existing among the species. The strains originated from different geographical and ecological niches (Malaysian, West African, North American, Wine/European and Sake) and represent clean, non-mosaic lineages of S. cerevisiae, meaning that their genomes differ essentially by monomorphic and private SNPs. In this study, one representative strain for each of the five S. cerevisiae clean lineages was selected and mutated for several auxotroph genes by clean markerless deletions, so that all dominant markers remained available for further genetic manipulations. A set of 50 strains was assembled, including eight haploid and two diploid strains for each lineage. These strains carry different combinations of leu2 increment 0, lys2 increment 0, met15 increment 0, ura3 increment 0 and/or ura3 increment ::KanMX-barcoded deletions with marker configurations resembling that of the BY series, which will allow large-scale crossing with existing deletion collections. This new set of genetically tractable strains provides a powerful tool kit to explore the impact of natural variation on complex biological processes

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries

International audienceMotivation: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. Results: Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes

Spen limits intestinal stem cell self-renewal.

Precise regulation of stem cell self-renewal and differentiation properties is essential for tissue homeostasis. Using the adult Drosophila intestine to study molecular mechanisms controlling stem cell properties, we identify the gene split-ends (spen) in a genetic screen as a novel regulator of intestinal stem cell fate (ISC). Spen family genes encode conserved RNA recognition motif-containing proteins that are reported to have roles in RNA splicing and transcriptional regulation. We demonstrate that spen acts at multiple points in the ISC lineage with an ISC-intrinsic function in controlling early commitment events of the stem cells and functions in terminally differentiated cells to further limit the proliferation of ISCs. Using two-color cell sorting of stem cells and their daughters, we characterize spen-dependent changes in RNA abundance and exon usage and find potential key regulators downstream of spen. Our work identifies spen as an important regulator of adult stem cells in the Drosophila intestine, provides new insight to Spen-family protein functions, and may also shed light on Spen's mode of action in other developmental contexts