Cédric Gobet
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View article: Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation Open
Background Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and valine, are essent…
View article: Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates
Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates Open
mRNA translation involves multiple regulatory steps, but how translation elongation in-fluences protein output remains unclear. Using SunTag live-cell imaging and mathematical modeling, we quantified translation dynamics in single mRNAs ac…
View article: Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates
Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates Open
mRNA translation involves multiple regulatory steps, but how translation elongation in-fluences protein output remains unclear. Using SunTag live-cell imaging and mathematical modeling, we quantified translation dynamics in single mRNAs ac…
View article: Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates
Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates Open
mRNA translation involves multiple regulatory steps, but how translation elongation in-fluences protein output remains unclear. Using SunTag live-cell imaging and mathematical modeling, we quantified translation dynamics in single mRNAs ac…
View article: Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation
Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation Open
Translation elongation plays a key role in cellular homeostasis, and dysregulation of this process has been implicated in various diseases and metabolic disorders. Uncovering the causes of intragenic heterogeneity of translation, especiall…
View article: Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation Open
Cells regulate protein synthesis in response to fluctuating nutrient availability through coordinated mechanisms that affect both translation initiation and elongation. Branched-chain amino acids (BCAAs)—leucine, isoleucine, and valine—are…
View article: A sexually dimorphic hepatic cycle of periportal VLDL generation and subsequent pericentral VLDLR-mediated re-uptake
A sexually dimorphic hepatic cycle of periportal VLDL generation and subsequent pericentral VLDLR-mediated re-uptake Open
Recent single-cell transcriptomes revealed spatiotemporal programmes of liver function on the sublobular scale. However, how sexual dimorphism affected this space-time logic remained poorly understood. We addressed this by performing scRNA…
View article: Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations
Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations Open
Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model rib…
View article: A sexually dimorphic hepatic cycle of periportal VLDL generation and subsequent pericentral VLDLR-mediated lipoprotein re-uptake
A sexually dimorphic hepatic cycle of periportal VLDL generation and subsequent pericentral VLDLR-mediated lipoprotein re-uptake Open
Recent single-cell transcriptomes revealed spatiotemporal programmes of liver function on the sublobular scale. However, how sexual dimorphism affected this space-time logic remained poorly understood. We addressed this by performing scRNA…
View article: Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior
Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior Open
The synchronization of circadian clock depends on a central pacemaker located in the suprachiasmatic nuclei. However, the potential feedback of peripheral signals on the central clock remains poorly characterized. To explore whether periph…
View article: Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans
Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans Open
The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) …
View article: Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human
Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human Open
Supplementary data
View article: Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human
Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human Open
Supplementary data
View article: Mice with humanized livers reveal the involvement of hepatocyte circadian clocks in rhythmic behavior and physiology
Mice with humanized livers reveal the involvement of hepatocyte circadian clocks in rhythmic behavior and physiology Open
The circadian clock is an evolutionarily acquired gene network that synchronizes physiological processes to adapt homeostasis to the succession of day and night. While most mammalian cells have a circadian clock, their synchronization at t…
View article: Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver
Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver Open
In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily…
View article: Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human
Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human Open
The circadian clock modulates most of human physiology. However, the organization of tissue-specific gene expression rhythms is still poorly known, as well as age and sex dependencies. We leveraged the Genotype-Tissue Expression project (G…
View article: Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human
Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human Open
Supplementary data as explained in the text
View article: Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human
Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human Open
Supplementary data
View article: Disruption of the circadian clock component BMAL1 elicits an endocrine adaption impacting on insulin sensitivity and liver disease
Disruption of the circadian clock component BMAL1 elicits an endocrine adaption impacting on insulin sensitivity and liver disease Open
Significance While increasing evidence associates the disruption of circadian rhythms with pathologic conditions, including obesity, type 2 diabetes, and nonalcoholic fatty liver diseases (NAFLD), the involved mechanisms are still poorly d…
View article: Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver
Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver Open
In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily…
View article: Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data
Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data Open
Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that …
View article: The integrated stress response contributes to tRNA synthetase–associated peripheral neuropathy
The integrated stress response contributes to tRNA synthetase–associated peripheral neuropathy Open
Defeating peripheral neuropathy The mechanisms underlying peripheral neuropathies are not well understood. Spaulding et al . studied mouse models of the inherited Charcot-Marie-Tooth (CMT) disease, which is caused by mutations in transfer …
View article: Comment on “Circadian rhythms in the absence of the clock gene <i>Bmal1</i> ”
Comment on “Circadian rhythms in the absence of the clock gene <i>Bmal1</i> ” Open
Ray et al . (Reports, 14 February 2020, p. 800) recently claimed temperature-compensated, free-running mRNA oscillations in Bmal1 –/– liver slices and skin fibroblasts. We reanalyzed these data and found far fewer reproducible mRNA oscilla…
View article: Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms
Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms Open
Significance The rotation of the Earth around its own axis creates daily changes in the environment for virtually all living organisms. To anticipate and adapt to those changes, mammals possess an evolutionarily conserved circadian clock t…
View article: What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis
What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis Open
Protein synthesis from mRNA is an energy-intensive and tightly controlled cellular process. Translation elongation is a well-coordinated, multifactorial step in translation that undergoes dynamic regulation owing to cellular state and envi…
View article: MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly
MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly Open
The glucose-sensing Mondo pathway regulates expression of metabolic genes in mammals. Here, we characterized its function in the zebrafish and revealed an unexpected role of this pathway in vertebrate embryonic development. We showed that …
View article: Author response: MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly
Author response: MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract The glucose-sensing Mondo pat…
View article: Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver
Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver Open
Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and trans…
View article: Modeling ribosome dwell times and relationships with tRNA loading and codon usage in mammals
Modeling ribosome dwell times and relationships with tRNA loading and codon usage in mammals Open
Protein translation depends on mRNA-specific initiation, elongation and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome an…