Publication
Circadian dynamics of RNA localisation in the mammalian liver
Related publications (122)
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Pancreatic cancer cells with limited access to free amino acids can grow by scavenging extracellular protein. In a murine model of pancreatic cancer, we performed a genome-wide CRISPR screen for genes required for scavenging-dependent growth. The screen id ...
2022Space-time logic of liver gene expression at sub-lobular scale
Felix Naef, Clémence Yumie Syloun Hurni, Colas Noé Droin
The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive tempo ...
NATURE RESEARCH2021Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle
Felix Naef, Jake Yeung, Jérôme Mermet
The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughou ...
2021LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis
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The recruitment of thermogenic brite adipocytes within white adipose tissue attenuates obesity and metabolic comorbidities, arousing interest in understanding the underlying regulatory mechanisms. The molecular network of brite adipogenesis, however, remai ...
WILEY2021The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy
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 ...
AMER ASSOC ADVANCEMENT SCIENCE2021Mitochondrial RNA granules are fluid condensates positioned by membrane dynamics
Phase separation concentrates mitochondrial RNA granules. Here Rey et al., show that mitochondrial RNA granules (MRGs) behaviour is consistent with liquid-liquid phase separation (LLPS) and their fusion coincides with mitochondrial remodelling. Mitochondri ...
NATURE RESEARCH2020Robust 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 ...
2020Detecting DNA and RNA and Differentiating Single-Nucleotide Variations via Field-Effect Transistors
Nako Nakatsuka, Yang Yang, Bowen Zhu
We detect short oligonucleotides and distinguish between sequences that differ by a single base, using label-free, electronic field-effect transistors (FETs). Our sensing platform utilizes ultrathin-film indium oxide FETs chemically functionalized with sin ...
2020The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Vassily Hatzimanikatis, Pierre Guy Rémy Salvy
Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...
2020The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism
Felix Naef, Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Jake Yeung
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