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Felix Naef

Related publications (104)

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Related publications (104)

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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

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

Pierre Gönczy, Felix Naef, Coralie Busso, Simon Blanchoud

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

Structure of silent transcription intervals and noise characteristics of mammalian genes

Felix Naef, Benjamin Zoller, Damien Lionel Nicolas

Mammalian transcription occurs stochastically in short bursts interspersed by silent intervals showing a refractory period. However, the underlying processes and consequences on fluctuations in gene products are poorly understood. Here, we use single allel ...

Nature / European Molecular Biology Organization2015

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

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

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 ...

Natl Acad Sciences2014

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

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

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

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

Felix Naef, Cédric Gobet, Kyle Gustafson, Mathieu Quinodoz

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

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, Cédric Gobet, Kyle Gustafson, Jonathan Bieler, 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

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics

Bart Deplancke, Felix Naef, Marc Moniatte, Adrian Schmid, Sunil Kumar Raghav, Irina Krier, Benjamin Zoller, Jovan Simicevic, Paola Alejandra Gilardoni

The cellular abundance of transcription factors (TFs) is an important determinant of their regulatory activities. Deriving TF copy numbers is therefore crucial to understanding how these proteins control gene expression. We describe a sensitive selected re ...

Nature Publishing Group2013

The Circadian Clock Coordinates Ribosome Biogenesis

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

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

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National Academy of Sciences2015

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

Felix Naef

Cédric Gobet

Patrick Descombes

Frédéric Bruno Martin Gachon

Benjamin Dieter Weger

Jingkui Wang

Florian Atger