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Felix Naef

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Publications associées (80)

Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells

Matthias Lütolf, Felix Naef, Eric Paquet, Yoji Tabata, Ambroise Roger Vuaridel, François Réal Rivest, Andrea Manfrin

Signaling centers, localized groups of cells that secrete morphogens, play a key role in early development and organogenesis by orchestrating spatial cell fate patterning. Here we present a microfluidic approach that exposes human pluripotent stem cell (hP ...

NATURE PUBLISHING GROUP2019

Low-dimensional dynamics of two coupled biological oscillators

Felix Naef, Eric Paquet, Colas Noé Droin

The circadian clock and the cell cycle are two biological oscillatory processes that coexist within individual cells. These two oscillators were found to interact, which can lead to their synchronization. Here, we develop a method to identify a low-dimensi ...

NATURE PUBLISHING GROUP2019

Differential regulation of RNA polymerase III genes during liver regeneration

Felix Naef, Philippe Jacquet, Nicolas Jean Philippe Guex, Jonathan Aryeh Sobel, Cristian Carmeli, Olivier Martin, Irina Krier, Mauro Delorenzi, Nouria Hernandez, Bart Deplancke, Jacques Rougemont, François Mange, Laura Symul, Fabrice David, Sunil Kumar Raghav, Julien Delafontaine, Marion Leleu, Julia Catharina Cajan, Winship Herr, Kyle Gustafson, Maykel Lopes, Dominic Villeneuve, Ioannis Xenarios

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Oxford University Press (OUP)2019

Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex

Felix Naef, Maxime Jan, Jake Yeung, Ioannis Xenarios

The timing and duration of sleep results from the interaction between a homeostatic sleep-wake-driven process and a periodic circadian process, and involves changes in gene regulation and expression. Unraveling the contributions of both processes and their ...

National Academy of Sciences2019

Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells

Felix Naef, Onur Tidin, David Michael Suter, Torgil Elias Friman

The transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcript ...

Nature Research2019

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

Modulation of transcriptional burst frequency by histone acetylation

Felix Naef, Benjamin Zoller, Damien Lionel Nicolas, David Michael Suter

National Academy of Sciences2018

Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

Felix Naef, Jake Yeung, Jérôme Mermet, Celine Jouffe, Frédéric Bruno Martin Gachon

Cold Spring Harbor Laboratory Press2018

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates

Felix Naef, Eric Paquet, David Michael Suter, Martina Biserni, Andrea Brigitta Alber

Cells need to reliably control their proteome composition to maintain homeostasis and regulate growth. How protein synthesis and degradation interplay to control protein expression levels remains unclear. Here, we combined a tandem fluorescent timer and pu ...

CELL PRESS2018

Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock

Felix Naef, Jake Yeung, Frédéric Bruno Martin Gachon

Mammalian physiology resonates with the daily changes in the external environment, allowing processes such as rest-activity cycles, metabolism, and body temperature to synchronize with daily changes in the surroundings. Studies have identified the molecula ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2018

Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior

Felix Naef, Jake Yeung

Circadian rhythms in physiology and behavior evolved to resonate with daily cycles in the external environment. In mammals, organs orchestrate temporal physiology over the 24-h day, which requires extensive gene expression rhythms targeted to the right tis ...

ELSEVIER SCIENCE LONDON2018

Long- and short-term molecular consequences of sleep loss in mice

Felix Naef, Jake Yeung

WILEY2018

Guidelines for Genome-Scale Analysis of Biological Rhythms

Felix Naef, Frédéric Bruno Martin Gachon, Zheng Chen, Alaaddin Bulak Arpat, Xiaodong Li, Han Wang

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods ...

Sage Publications Inc2017

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

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

Felix Naef, Loïc Dayon, Martin Kussmann, Jingkui Wang, Florian Atger, Daniel Alain Dominique Marie Mauvoisin, Frédéric Bruno Martin Gachon, Federico Sizzano

Diurnal oscillations of gene expression controlled by the circadian clock and its connected feeding rhythm enable organisms to coordinate their physiologies with daily environmental cycles. While available techniques yielded crucial insights into regulatio ...

Cell Press2017

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Felix Naef, Jake Yeung, Jérôme Mermet

Mammals have evolved an internal timing system, the circadian clock, which synchronizes physiology and behavior to the daily light and dark cycles of the Earth. The master clock, located in the suprachiasmatic nucleus (SCN) of the brain, takes fluctuating ...

Cold Spring Harbor Lab Press, Publications Dept2017

What shapes eukaryotic transcriptional bursting?

Felix Naef, Damien Lionel Nicolas, Nicholas Edward Phillips

Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous p ...

Royal Society of Chemistry2017

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Felix Naef, Jonathan Aryeh Sobel, Guillaume Rey, Irina Krier, Nouria Hernandez, Bart Deplancke, Matteo Dal Peraro, Sunil Kumar Raghav, Frédéric Bruno Martin Gachon, Alexandra Styliani Kalantzi, Benjamin Dieter Weger

Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles ...

Public Library of Science2017

A new promoter element associated with daily time keeping in Drosophila

Felix Naef, Eric Paquet

Circadian clocks are autonomous daily timekeeping mechanisms that allow organisms to adapt to environmental rhythms as well as temporally organize biological functions. Clock-controlled timekeeping involves extensive regulation of rhythmic gene expression. ...

Oxford University Press2017

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