Publications by David Michael Suter

Orchestration of pluripotent stem cell genome reactivation during mitotic exit

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

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

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