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Felix Naef

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Publications associées (80)

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

Felix Naef, Loïc Dayon, Carlos Canto Alvarez, Martin Kussmann, Jingkui Wang, Sebastiano Collino, Florian Atger, Daniel Alain Dominique Marie Mauvoisin, Frédéric Bruno Martin Gachon, Joanna Ratajczak

Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is t ...

Elsevier2017

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Felix Naef, Daniel Boss, Mirko Bischofberger, Françoise Gisou van der Goot Grunberg, Mircea Ioan Iacovache

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their jou ...

Elsevier2016

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp

Felix Naef, Saeed Omidi Klishami

In mammals, body temperature fluctuates diurnally around a mean value of 36 degrees C-37 degrees C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, ...

Cold Spring Harbor Laboratory2016

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Felix Naef, Simon Blanchoud, Benjamin Zoller, Damien Lionel Nicolas, Onur Tidin

Fluorescence and bioluminescence time-lapse imaging allows to investigate a vast range of cellular processes at single-cell or even subcellular resolution. In particular, time-lapse imaging can provide uniquely detailed information on the fine kinetics of ...

Academic Press Inc Elsevier Science2015

Quantitative Analysis and Modeling Probe Polarity Establishment in C. elegans Embryos

Felix Naef, Simon Blanchoud, Pierre Gönczy, Coralie Busso

Cell polarity underlies many aspects of metazoan development and homeostasis, and relies notably on a set of PAR proteins located at the cell cortex. How these proteins interact in space and time remains incompletely understood. We performed a quantitative ...

Cell Press2015

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

Felix Naef, Patrick Descombes, Cédric Gobet, Jingkui Wang, Florian Atger, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. Although rhythmic mRNA accumulation has been exte ...

National Academy of Sciences2015

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

Felix Naef, Cédric Gobet, Mathieu Quinodoz, Kyle Gustafson

Background: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles th ...

BioMed Central2014

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

Felix Naef, Jingkui Wang, Florian Atger, Celine Jouffe, Daniel Alain Dominique Marie Mauvoisin, Frédéric Bruno Martin Gachon

Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known ab ...

National Academy of Sciences2014

Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells

Felix Naef, Laura Symul

U2OS cells harbor a circadian clock but express only a few rhythmic genes in constant conditions. We identified 3040 binding sites of the circadian regulators BMAL1, CLOCK and CRY1 in the U2OS genome. Most binding sites even in promoters do not correlate w ...

Public Library of Science2014

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

Felix Naef, Jonathan Bieler, Cédric Gobet, Kyle Gustafson, Rosamaria Cannavo

Circadian cycles and cell cycles are two fundamental periodic processes with a period in the range of 1 day. Consequently, coupling between such cycles can lead to synchronization. Here, we estimated the mutual interactions between the two oscillators by t ...

Nature / European Molecular Biology Organization2014

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Felix Naef, Philippe Jacquet, Nicolas Dénervaud, Sebastian Maerkl, Jacques Rougemont, Marcel Geertz

In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we ...

Cold Spring Harbor Laboratory Press2014

The Circadian Clock Coordinates Ribosome Biogenesis

Felix Naef, Laura Symul, Florian Atger, Celine Jouffe, Frédéric Bruno Martin Gachon

Biological rhythms play a fundamental role in the physiology and behavior of most living organisms. Rhythmic circadian expression of clock-controlled genes is orchestrated by a molecular clock that relies on interconnected negative feedback loops of transc ...

Public Library Science2013

A chemostat array enables the spatio-temporal analysis of the yeast proteome

Felix Naef, Michaël Unser, Nicolas Dénervaud, Sebastian Maerkl, Ricard Delgado Gonzalo, Arun Stephen Rajkumar, Johannes Becker

Observing cellular responses to perturbations is central to generating and testing hypotheses in biology. We developed a massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min t ...

National Academy of Sciences2013

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

Felix Naef, Benjamin Zoller, Rosamaria Cannavo, David Michael Suter

Mammalian genes are often transcribed discontinuously as short bursts of RNA synthesis followed by longer silent periods. However, how these "on" and "off" transitions, together with the burst sizes, are modulated in single cells to increase gene expressio ...

National Academy of Sciences2013

Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome

Felix Naef, David Michael Suter

The transcription factors BMAL1 and CLOCK drive the circadian transcription of clock and clock-controlled genes, such as Dbp. To investigate the kinetics of BMAL1 binding to target genes in real time, we generated a cell line harboring tandem arrays of Dbp ...

Elsevier2012

Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally

Felix Naef, Guillaume Rey

In mammalian tissues, circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. We show that simulated body temperature cycles, but not peripheral oscillators, contro ...

American Association for the Advancement of Science2012

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

Felix Naef, Nicolas Jean Philippe Guex, Olivier Martin, Mauro Delorenzi, Nouria Hernandez, Bart Deplancke, Jacques Rougemont, Laura Symul, Winship Herr

Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we gener ...

Public Library Science2012

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

Felix Naef, Guillaume Rey, Jacques Rougemont

The mammalian circadian clock uses interlocked negative feedback loops in which the heterodimeric basic helix-loop-helix transcription factor BMAL1/CLOCK is a master regulator. While there is prominent control of liver functions by the circadian clock, the ...

2011

Mammalian genes are transcribed with widely different bursting kinetics

Felix Naef, David Michael Suter

In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods called transcriptional bursts, interspersed by silent intervals. We describe how such bursts generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis ...

American Association for the Advancement of Science2011

Origins and consequences of transcriptional discontinuity

Felix Naef, David Michael Suter

In both prokaryotes and eukaryotes, transcription has been described as being temporally discontinuous, most genes being active mainly during short activity windows interspersed by silent periods. In mammalian cells, recent studies performed at the single ...

2011

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