The budding yeast heterochromatic SIR complex resets upon exit from stationary phase

The budding yeast SIR complex (Silent Information Regulator) is the principal actor in heterochromatin formation, which causes epigenetically regulated gene silencing phenotypes. The maternal chromatin bound SIR complex is disassembled during replication. Consequently, if heterochromatin is to be restored on both daughter strands, the SIR complex has to be reformed on both strands to pre-replication levels. The dynamics of SIR complex maintenance and reformation during the cell-cycle and in different growth conditions are however not clear. Understanding exchange rates of SIR subunits during the cell cycle and their distribution pattern to daughter chromatids after replication has important implications for how heterochromatic states may be inherited and therefore how epigenetic states are maintained from one cellular generation to the next. We used the tag switch RITE system to measure genome wide turnover rates of the SIR subunit Sir3 before and after exit from stationary phase and show that maternal Sir3 subunits are completely replaced with newly synthesized Sir3 at subtelomeric regions during the first cell cycle after release from stationary phase. The SIR complex is therefore not "inherited" and the silenced state has to be established de novo upon exit from stationary phase. Additionally, our analysis of genome-wide transcription dynamics shows that precise Sir3 dosage is needed for the optimal up-regulation of "growth" genes during the first cell-cycle after release from stationary phase

Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast

Dynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin. Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. We find that H3K56Ac is a genome-wide activator of transcription. While H3K56Ac has a major impact on transcription initiation, it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly. We also detect a stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, a single histone mark can exert both positive and negative impacts on transcription that are coupled to different cell cycle events

Inheritance of Chromatin Proteins in Budding Yeast: metabolic gene regulators TUP1, FPR4 and Rpd3L are retained in the mother cell

Asymmetric division is a prerequisite for cellular differentiation. Phenotypic transformation during differentiation is a poorly understood epigenetic phenomenon, in which chromatin theoretically plays a role. The assumption that chromatin components segregate asymmetrically in asymmetric divisions has however not been systematically tested. We have developed a live cell imaging method to measure how 18 chromatin proteins are inherited in asymmetric divisions of budding yeast. We show that abundant and moderately abundant maternal proteins segregate stochastically and symmetrically between the two cells with the exception of Rxt3, Fpr4 and Tup1, which are retained in the mother. Mother retention seems to be the norm for low abundance proteins with the exception of Sir2 and the linker histone H1. Our in vivo analysis of chromatin protein behavior in single cells highlights general trends in protein biology during the cell cycle such as coupled protein synthesis and decay, and a correlation between half-lives and cell cycle duration

Inégalités sociétales et exposome urbain. Des origines sociales pour des expositions différentes

Deguen S, Vasseur P, Kihal-Talantikite W. Exposome et inégalités environnementales. Science/Médecine, 2021International audienceToday, many epidemiological studies have proved the adverse health consequences of environmental exposure. For instance, air pollution exposure is recognized to be related with respiratory and cardiovascular diseases as well as adverse pregnancy outcomes. Noise nuisances are also known to increase cardiovascular diseases and to disturb the sleeping quality. Inversely, the access and availability of various resources, as parks, green spaces, and playgrounds positively affect health, psychological and physical well-being, and favorable health behaviors. In this present literature review, we will focus on the urban dimension of exposome, defined by Robinson et al. as the accumulation of all urban settings favorable or unfavorable to health, from the time of life in utero.Les études épidémiologiques sont nombreuses aujourd’hui à révéler l’association entre des facteurs d’exposition environnementale et des problèmes de santé, aigus comme chroniques, et survenant à différents stades de la vie. Citons, par exemple, l'exposition à la pollution de l'air associée à de nombreuses infections respiratoires, maladies cardiovasculaires et à certaines issues défavorables de la grossesse. L’exposition aux nuisances sonores est également reconnue comme pouvant augmenter le risque de maladies cardiovasculaires et perturber la qualité du sommeil. Inversement, l’accès et la disponibilité de certaines ressources, comme les parcs, les aires de jeux, ou les espaces verts sont reconnus pour être associés à un meilleur état de santé, de bien-être physique et psychique et à des comportements favorables à la santé. Dans cette Synthèse, nous nous intéresserons plus particulièrement à l’exposome dit « urbain », défini par Robinson et al. comme l'ensemble des éléments de l’environnement urbain favorables et défavorables à la santé, et ce, dès la vie in utero

Protocol for tracking the inheritance patterns of proteins in live Saccharomyces cerevisiae cells using a photo-convertible fluorescent protein

Summary: Tracking the inheritance patterns of proteins (TrIPP) is a live-cell imaging technique used for tracking maternal protein segregation patterns between mother and daughter cells during asymmetric divisions of budding yeast. We use the photo-convertible fluorescent protein Dendra2 fused to a protein of interest (POI). Irreversible conversion from green to red fluorescence allows for parallel monitoring of old and new proteins for several generations. Single-cell quantitative image analysis of time-lapse microscopy gives synthesis and decay rates, as well as segregation patterns of the POI.For complete details on the use and execution of this protocol, please refer to Auboiron et al. (2021)

Time constant of hydraulic-head response in aquifers subjectedto sudden recharge change: application to large basins

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Effets de la conduite du séchage sur la qualité des pâtes alimentaires

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Dynamics of Nucleosome Positioning Maturation following Genomic Replication

Chromatin is thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture occurring during genomic replication. Here, we measure a key aspect of chromatin structure dynamics during replication—how rapidly nucleosome positions are established on the newly replicated daughter genomes. By isolating newly synthesized DNA marked with 5-ethynyl-2′-deoxyuridine (EdU), we characterize nucleosome positions on both daughter genomes of S. cerevisiae during chromatin maturation. We find that nucleosomes rapidly adopt their mid-log positions at highly transcribed genes, which is consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in hir1Δ mutants reveal a role for HIR in nucleosome spacing. We also characterized nucleosome positions on the leading and lagging strands, uncovering differences in chromatin maturation dynamics at hundreds of genes. Our data define the maturation dynamics of newly replicated chromatin and support a role for transcription in sculpting the chromatin template

Vegetarian and Vegan Diets: Beliefs and Attitudes of General Practitioners and Pediatricians in France

International audienceStudies suggest a decreasing trend in the consumption of meat products and a growing interest in vegetarian diets. Medical support may be relevant, especially when switching to a vegan diet. Our objective was to describe the beliefs and attitudes of primary care physicians toward vegetarian diets. A cross-sectional survey was conducted among general practitioners and pediatricians thorough a questionnaire including socio-demographic characteristics, specific care to vegetarians, and the risks and benefits of vegetarian diets according to physicians. Out of the 177 participating physicians, 104 (59%) have seen at least one vegetarian patient in consultation in the last three months. Half of the physicians declared that they would dissuade their patients from switching to a vegan diet (n = 88, 51%) and 14% (n = 24) from switching to an ovo-lacto-vegetarian (OLV) diet. Most physicians (n = 141, 88%) did not feel informed enough about these diets. Physicians thought that the most frequent deficiencies for OLV and vegan diets were iron (76% and 84%, respectively) and protein (45% and 79%, respectively). These results highlight the fact that French primary care physicians feel concerned by this subject and need more information on these diets. Specific recommendations would be useful to support their practice and relationship with vegetarians

Dietary Patterns, Ultra-processed Food, and the Risk of Inflammatory Bowel Diseases in the NutriNet-Santé Cohort

International audienceBackgroundThe incidence of inflammatory bowel diseases (IBDs) tended to increase for several decades. Diet is suspected to be a major determinant of the occurrence of these diseases. This prospective study aimed to assess the associations among occurrence of IBD, dietary patterns, and ultra-processed food in the French NutriNet-Santé cohort.MethodsParticipants of the NutriNet-Santé cohort who completed at least three 24-hour dietary records were included. Incident IBD cases were identified from 3 questionnaires and confirmed by phone or email interview. Major dietary patterns (DPs) were computed using a principal component analysis (PCA) based on 29 food groups’ consumption, whereas proportions of ultra-processed foods (UPFs) were obtained using the NOVA classification. Multivariable Poisson models were performed to evaluate associations among DP quintiles, UPF proportion (UPFp) in the diet, and incident IBD.ResultsA total of 105,832 participants were included, contributing 238,924 person-years in a mean follow-up of 2.3 ± 2.2 years. Among them, 75 participants reported an incident IBD. Three major DPs were retained: “healthy,” “traditional,” and “western.” No significant association was found for DPs and UPFp after adjustments for covariates.ConclusionsIn this study, neither DPs nor UPF proportion in the diet were significantly associated with the risk of incident IBD after adjustments for covariates. Further studies are needed to investigate the long-term association between diet and IBD