Break-induced replication (BIR) is a highly mutagenic eukaryotic homologous DNA recombination pathway that repairs one-ended DNA double strand breaks such as broken DNA replication forks and eroded telomeres. While searching for cis-acting factors regulating ectopic BIR efficiency, we found that ectopic BIR efficiency is the highest close to chromosome ends. The variations of ectopic BIR efficiency as a function of the length of DNA to replicate can be described as a combination of two decreasing exponential functions, a property in line with repeated cycles of strand invasion, elongation and dissociation that characterize BIR. Interestingly, the apparent processivity of ectopic BIR depends on the length of DNA already synthesized. Ectopic BIR is more susceptible to disruption during the synthesis of the first ~35–40 kb of DNA than later, notably when the template chromatid is being transcribed or heterochromatic. Finally, we show that the Srs2 helicase promotes ectopic BIR from both telomere proximal and telomere distal regions in diploid cells but only from telomere proximal sites in haploid cells. Altogether, we bring new light on the factors impacting a last resort DNA repair pathway.
Background: The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest within the field of paleogenetics, as a means of deciphering the social organization of past societies. However, kinship analyses are in practice often quite difficult to apply within paleogenetic studies, and may carry a high degree of uncertainty in the results they provide, especially when applied on low coverage and/or highly degraded samples, or when studying poorly characterized populations. To overcome these challenges, most of the available kinship estimation methods either refrain from inferring ties beyond the second degree (e.g., half-siblings), and/or rely on the use of a cohort of individuals to obtain a satisfactory statistical significance. Thus, the current state of the art remains intrinsically limited when attempting to estimate kinship on a small number of individuals, or when trying to detect more distant relationships (e.g., cousins). Methods:Here, we present GRUPS-rs:an update and complete reimplementation of GRUPS (Get Relatedness Using Pedigree Simulations), an ancient DNA kinship estimation software based on the methods originally developed in (Martin et al. 2017).GRUPS-rs both computes an estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of a cohort of individuals. Results: We highlight that GRUPS and GRUPS-rs are especially suitable to perform kinship analysis on a restricted number of ancient samples, and can provide a sufficient statistical significance to estimate genetic relatedness past the second degree, while taking into account user-defined contamination and sequencing error estimates. Importantly, GRUPS-rs offers an estimated 14000-fold speed-up in runtime performance compared to its predecessor — allowing the joint estimation of kinship between dozens of individuals in a matter of minutes — and is now bundled with a user-friendly Shiny interface, in which users can interactively visualize their results. Conclusions: The GRUPS kinship estimation method is now fully operational in its "GRUPS-rs" implementation, whose use is particularly recommended when analyzing a restricted number of low coverage DNA samples.
Recent work has demonstrated a repressive effect of chromatin on the transcription of the yeast SNR6 gene in vitro. Here, we show the relations between chromatin structure and transcriptional activity of this gene in vivo. Analysis of the SNR6 locus by micrococcal nuclease digestion showed a protection of the TATA box, nuclease-sensitive sites around the A and B blocks, and arrays of positioned nucleosomes in the flanking regions. Analysis of a transcriptionally silent SNR6 mutant containing a 2-bp deletion in the B block showed a loss of TATA-protection and rearrangement or destabilization of nucleosomes in the flanking regions. Hence, SNR6 organizes the chromatin structure in the whole region in a manner dependent on its transcriptional state. Transcriptional analysis was performed by use of maxi-gene SNR6 constructs introduced into histone-mutated strains. Chromatin disruption induced by histone H4 depletion stimulated the transcription of promoter-deficient, but not of wild-type SNR6 genes, revealing a competition between the formation of nucleosomes and the assembly of Pol III transcription complexes that was much in favor of transcription factors. On the other hand, amino-terminal mutations in histone H3 or H4 had no effect (H4) or only a moderate stimulatory effect (H3) on the transcription of promoter-deficient SNR6 genes.
Abstract RAD53 encodes a conserved protein kinase that acts as a central transducer in the DNA damage and the DNA replication checkpoint pathways in Saccharomyces cerevisiae. To identify new elements of these pathways acting with or downstream of RAD53, we searched for genes whose overexpression suppressed the toxicity of a dominant-lethal form of RAD53 and identified PTC2, which encodes a protein phosphatase of the PP2C family. PTC2 overexpression induces hypersensitivity to genotoxic agents in wild-type cells and is lethal to rad53, mec1, and dun1 mutants with low ribonucleotide reductase activity. Deleting PTC2 specifically suppresses the hydroxyurea hypersensitivity of mec1 mutants and the lethality of mec1Δ. PTC2 is thus implicated in one or several functions related to RAD53, MEC1, and the DNA checkpoint pathways.
Like all modern Romance languages, French has a sex-based grammatical gender with two genders, feminine and masculine, and a lexicon that is highly sex-differentiated. These characteristics give rise to a number of issues, including the problematic generic use of the masculine grammatical gender, coupled with the challenge of sex categorization itself, and the epistemological difficulty of an adequate sociological description and analysis of what gender commonsense categories really are about. To remedy these concerns, several authors have proposed the creation of an additional, epicene grammatical gender. We have identified three such systematic proposals, or solutions, which specify various morphological options for new epicene nouns and gender markers on their satellite elements. These options include the use of non-standard or rarely used characters, the merging of feminine and masculine gender markers, as well as consonantal and vowel changes. In the simplest proposal, referred to as “solution I,” new epicene forms are mostly derived from feminine forms by systematically replacing with an i the final e that generally differentiates feminines from their masculine counterparts in written French. Although these solutions are used in some communities, their learnability has not been addressed so far, even though it could be a determining factor in their popularity and their eventual integration into standard French. In the present study, we provide a first assessment of this aspect by means of an online translation test. For each solution, French-speaking participants were instructed that they would be trained to learn an “alien” language that does not mark sex/gender categories (these alien languages correspond to standard French where only gendered words referring to people are replaced by the new epicene forms recommended by each solution). After a short learning-by-example phase, participants were required to translate into the alien language a set of 16 standard French sentences. The translations were analyzed as a function of several variables including the participants’ self-reported age and sex, the word categories and the solutions themselves. While all solutions proved quickly learnable, participants’ responses with solution I achieved the highest accuracy score, in particular with regard to the production of non-standard epicene forms.
Afin d'obtenir des informations sur la diversité génétique et l'alimentation de l'hyène des cavernes, nous avons analysé l'ADN de coprolithes de six sites du sud de la France. Les sites correspondent à quatre grottes ardéchoises (Grotte‑aux‑Ours de Châteaubourg, Baume Néron et Trou‑du‑Renard de Soyons, Le Figuier) et deux grottes de l'Aude (Tournal, La Crouzade). Pour huit coprolithes de ces six sites, nous avons réalisé un séquençage global massif qui a livré à partir de chaque échantillon des lectures pour 60 à 250 millions de fragments d'ADN. La recherche de fragments du génome mitochondrial de 35 espèces animales, dont l'Homme, montre que l'ADN le plus abondant est systématiquement celui de l'hyène, ce qui valide l'identification des échantillons comme coprolithes d'hyène des cavernes. L'ADN d'autres espèces détecté dans les coprolithes indique la consommation par l'hyène de différents grands mamifères dont le cheval et le bison (Néron), l'ours des cavernes (Trou‑du‑Renard), le renne (Tournal) et le rhinocéros laineux (Le Figuier). Les raisons pour lesquelles les autres coprolithes ne livrent pas d'information sur l'alimentation de l'hyène sont discutées. L'analyse phylogénétique des séquences des génomes mitochondriaux d'hyène reconstruits à partir de l'ADN des coprolithes révèle la présence (Néron) d'un spécimen de l'haplogroupe B, détecté pour la première fois en France, alors que les autres spécimens appartiennent à l'haplogroupe A. La détermination de l'âge de trois coprolithes par la méthode du radiocarbone les situe à l'Aurignacien (Châteaubourg, 39 670‑38 000 cal. BP) ou au Gravettien (site de Soyons : Néron, 30 890‑30180 cal. BP ; Trou‑du‑Renard, 25 800‑25 290 cal. BP) suggérant, pour le site de Soyons, le possible remplacement durant le Gravettien de l'haplogroupe B par l'haplogroupe A. Nous montrons que l'haplogroupe A, constitué de génomes mitochondriaux d'hyènes des cavernes et d'hyènes tachetées actuelles, a une structuration plus complexe que celle envisagée précédemment. L'analyse des génomes nucléaires d'hyènes des cavernes et d'hyènes actuelles tachetées révèle une phylogénie différente de celle fournie par les génomes mitochondriaux. Les génomes nucléaires d'hyènes tachetées actuelles et d'hyènes des cavernes sont en effet répartis dans deux clades monophylétiques et, à l'intérieur du clade des hyènes des cavernes, le faible support pour le regroupement des spécimens en fonction de leur haplogroupe mitochondrial résulte probablement de flux géniques entre ces différents groupes et de tris de lignées incomplets.
