Publications de Cédric Gobet | EPFL Graph Search

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Felix Naef, Pierre Vandergheynst, Cédric Gobet, Mohan Vamsi Nallapareddy, Francesco Craighero

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 ribosome densities, ...

PMLR2024

Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior

Cédric Gobet, Sylviane Métairon, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

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 peripheral organ circad ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

Felix Naef, Cédric Gobet, Lorenzo Talamanca

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) project with an a ...

American Association for the Advancement of Science2023

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Felix Naef, Cédric Gobet, Clémence Yumie Syloun Hurni, Benjamin Dieter Weger

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 fluctuations of ...

PUBLIC LIBRARY SCIENCE2022

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Felix Naef, Cédric Gobet

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 have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

Comment on "Circadian rhythms in the absence of the clock gene Bmal1"

Felix Naef, Cédric Gobet

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 oscillations in this gen ...

American Association for the Advancement of Science2021

The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy

Yu Bai, Cédric Gobet, René Uwe Schneider

Dominant mutations in ubiquitously expressed transfer RNA (tRNA) synthetase genes cause axonal peripheral neuropathy, accounting for at least six forms of Charcot-Marie-Tooth (CMT) disease. Genetic evidence in mouse and Drosophila models suggests a gain-of ...

American Association for the Advancement of Science2021

Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms

Felix Naef, Cédric Gobet, Fabrice David, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Nicholas Edward Phillips

The circadian clock and feeding rhythms are both important regulators of rhythmic gene expression in the liver. To further dissect the respective contributions of feeding and the clock, we analyzed differential rhythmicity of liver tissue samples across se ...

National Academy of Sciences2021

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Felix Naef, Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Nagammal Neelagandan

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 transfer RNA (tRNA) pr ...

National Academy of Sciences2020

What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis

Felix Naef, Cédric Gobet, Nagammal Neelagandan

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 environmental determi ...

ROYAL SOC2020

The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism

Felix Naef, Cédric Gobet, Jake Yeung, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

The circadian clock and associated feeding rhythms have a profound impact on metabolism and the gut microbiome. To what extent microbiota reciprocally affect daily rhythms of physiology in the host remains elusive. Here, we analyzed transcriptome and metab ...

Cell Press2019

Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver

Felix Naef, Jonathan Aryeh Sobel, Cédric Gobet, Laura Symul, Jake Yeung, Jingkui Wang

National Academy of Sciences2018

Clock-dependent chromatin topology modulates circadian transcription and behavior

Felix Naef, Cédric Gobet, Damien Lionel Nicolas, Kyle Gustafson, Jake Yeung, Clémence Yumie Syloun Hurni, Jérôme Mermet, Celine Jouffe, Daniel Alain Dominique Marie Mauvoisin, Frédéric Bruno Martin Gachon

Cold Spring Harbor Laboratory Press2018

Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle

Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

2018

Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver

Cédric Gobet

Circadian rhythms allow organisms to anticipate and adapt to periodic environmental changes related to the day-night cycle. These rhythms originate from a genetic network ticking in almost every cell of our body and the coordination between different organ ...

EPFL2018

Pancreatic α- and β-Cellular Clocks Have Distinct Molecular Properties and Impact on Islet Hormone Secretion and Gene Expression

Michaël Unser, Daniel Sage, Cédric Gobet, Frédéric Bruno Martin Gachon

A critical role of circadian oscillators in orchestrating insulin secretion and islet gene transcription has been demonstrated recently. However, these studies focused on whole islets and did not explore the interplay between α-cell and β-cell clocks. We p ...

2017

Regulation of Mammalian Physiology by interconnected Circadian and Feeding Rhythms

Cédric Gobet, Florian Atger, Daniel Alain Dominique Marie Mauvoisin, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

Circadian clocks are endogenous timekeeping systems that adapt in an anticipatory fashion the physiology and behavior of most living organisms. In mammals, the master pacemaker resides in the suprachiasmatic nucleus and entrains peripheral clocks using a w ...

Frontiers Media Sa2017

Ribosome profiling and dynamic regulation of translation in mammals

Felix Naef, Cédric Gobet

Protein synthesis is an energy-demanding cellular process. Consequently, a well-timed, fine-tuned and plastic regulation of translation is needed to adjust and maintain cell states under dynamically changing environments. Genome-wide monitoring of translat ...

Elsevier2017

Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids

Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Meltem Weger

Altered daily patterns of hormone action are suspected to contribute to metabolic disease. It is poorly understood how the adrenal glucocorticoid hormones contribute to the coordination of daily global patterns of transcription and metabolism. Here, we exa ...

Public Library Science2016

Perturbed rhythmic activation of signaling pathways in mice deficient for Sterol Carrier Protein 2-dependent diurnal lipid transport and metabolism

Cédric Gobet, Sylviane Métairon, Celine Jouffe, Frédéric Bruno Martin Gachon, Mojgan Masoodi

Through evolution, most of the living species have acquired a time keeping system to anticipate daily changes caused by the rotation of the Earth. In all of the systems this pacemaker is based on a molecular transcriptional/translational negative feedback ...

Nature Research2016