Publications by David Michael Suter

Orchestration of pluripotent stem cell genome reactivation during mitotic exit

Cédric Deluz, David Michael Suter, Silja Michelle Placzek, Ludovica Vanzan

Cell identity maintenance faces many challenges during mitosis, as most DNA-binding proteins are evicted from DNA and transcription is virtually abolished. How cells maintain their identity through division and faithfully re-initiate gene expression during ...

2025

ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition

David Michael Suter

Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functio ...

2024

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

David Michael Suter, Natalya Katanayeva

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

National Academy of Sciences2024

Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets

David Michael Suter

Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has transformed our understanding of differentiation during development, regeneration, and disease. However, lineage tracing is technically demanding, often restricted in tim ...

Nature Portfolio2024

An out-of-equilibrium definition of protein turnover

David Michael Suter, Benjamin Joao Clément Antonin Hadrien Martin

Protein turnover (PT) has been formally defined only in equilibrium conditions, which is ill-suited to quantify PT during dynamic processes that occur during embryogenesis or (extra) cellular signaling. In this Hypothesis, we propose a definition of PT in ...

2023

Individual activator and repressor transcription factors act as modulators of global chromatin mobility

David Michael Suter

CELL PRESS2023

Target search dynamics of Sox transcription factors

Beat Fierz, David Michael Suter, Sim Sakong

CELL PRESS2023

Gene expression flux analysis reveals specific regulatory modalities of gene expression

David Michael Suter, Benjamin Joao Clément Antonin Hadrien Martin

The level of a given protein is determined by the synthesis and degradation rates of its mRNA and protein. While several studies have quantified the contribution of different gene expression steps in regulating protein levels, these are limited by using eq ...

2023

Transcription Factors and DNA Play Hide and Seek

David Michael Suter

Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depen ...

2020

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

Suliana Manley, Aleksandr Benke, Beat Fierz, Andrea Callegari, David Michael Suter, Christian Sieben

Transcription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by recognizing and binding to specific DNA promoter sequences. In higher eukaryotes, it remains unclear how the duration of TF binding to DNA relates to downstream tran ...

2019

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

Memory and relatedness of transcriptional activity in mammalian cell lineages

Felix Naef, David Michael Suter, Aleksandra Mandic, Saeed Omidi Klishami, Nicholas Edward Phillips

Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combine live- ...

Nature Research2019

Mitotic chromosome binding predicts transcription factor properties in interphase

Cédric Deluz, Mahé Cécile Raccaud, David Michael Suter, Andrea Brigitta Alber, Torgil Elias Friman

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The as ...

Nature Research2019

Dynamics of protein synthesis and degradation through the cell cycle

David Michael Suter, Andrea Brigitta Alber

Protein expression levels depend on the balance between their synthesis and degradation rates. Even quiescent (G(0)) cells display a continuous turnover of proteins, despite protein levels remaining largely constant over time. In cycling cells, global prot ...

TAYLOR & FRANCIS INC2019

Endogenous fluctuations of OCT 4 and SOX 2 bias pluripotent cell fate decisions

Cédric Deluz, David Michael Suter, Daniel Strebinger, Andrea Brigitta Alber, Torgil Elias Friman, Subashika Govindan

SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self‐renewal and differentiation. How temporal fluctuations in their expression levels bias lineage commitment is unknown. Here, we generated knock‐in reporter f ...

2019

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

Cédric Deluz, Bart Deplancke, David Michael Suter, Antonio Carlos Alves Meireles Filho, Torgil Elias Friman, Vincent Roland Julien Gardeux, Subashika Govindan

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewi ...

2019

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

David Michael Suter

Graph Chatbot

Orchestration of pluripotent stem cell genome reactivation during mitotic exit

ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets

An out-of-equilibrium definition of protein turnover

Individual activator and repressor transcription factors act as modulators of global chromatin mobility

Target search dynamics of Sox transcription factors

Gene expression flux analysis reveals specific regulatory modalities of gene expression

Transcription Factors and DNA Play Hide and Seek

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

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

Memory and relatedness of transcriptional activity in mammalian cell lineages

Mitotic chromosome binding predicts transcription factor properties in interphase

Dynamics of protein synthesis and degradation through the cell cycle

Endogenous fluctuations of OCT 4 and SOX 2 bias pluripotent cell fate decisions

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

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

Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells

Modulation of transcriptional burst frequency by histone acetylation

Single-Cell Quantification of Protein Degradation Rates by Time-Lapse Fluorescence Microscopy in Adherent Cell Culture