EPFL BioE Talks SERIES "Cooperativity and Antagonisms in Transcription Regulation"


Event details

Date 11.12.2023
Hour 16:0017:00
Speaker Arnaud Krebs, Ph.D., Group Leader, Genome Biology Unit, EMBL, Heidelberg (DE)
Location Online
Category Conferences - Seminars
Event Language English

Transcription factors (TFs) bind at cis-regulatory elements (CREs) such as enhancers and promoters to activate transcription. In higher eukaryotes, chromatin presents a physical barrier that needs to be overcome by TFs to access their DNA recognition motifs and activate transcription. Cooperativity is assumed to be a key mechanism for TFs to outcompete nucleosomes. Yet, the contribution of individual TFs to chromatin accessibility at CREs, and how their functions are assembled is currently not understood.

Current bulk assays used to map TF occupancy average binding events arising from millions of individual cells, not informing on the potential cooperativity and the antagonisms that organize their binding at CRE. To move beyond this boundary, we developed Single Molecule Footprinting (SMF) to quantify the binding of TFs at mouse regulatory regions. The method allows to simultaneously measure the occurrence of multiple TFs, nucleosomes and DNA methylation on individual molecules genome wide. I will illustrate how we leveraged this new layer of information to understand mechanisms of TF cooperativity and dissect the basic assembly rules used by TFs to open chromatin at CREs.

Detecting multiple TF binding events on single DNA molecules has enabled us to determine TF co-binding frequencies in vivo and to elucidate the underlying cooperative binding mechanism (Sönmezer et al, 2021). We now leveraged SMF’s ability to determine the width, and the frequency of nucleosome-free DNA occurring upon binding of individual or defined combination of TFs. To infer causality in the process, we leveraged F1 hybrids that contain genetic variants that disrupt TF binding motifs on individual alleles. I will show how unbound TF motifs are exposed within 80bp-long stretches of accessible DNA in about one third of the cells of the population. In contrast TF-bound molecules show longer nucleosome-free DNA (>100bp). Binding of individual TFs leads to chromatin accessibility in only a small fraction of cells (<20%). We find that additive and multiplicative assembly of TF chromatin-opening functions are required to explain the frequency of accessibility observed at CRE, and identify the assembly rules using high-throughput genome engineering. In summary, we identify the quantitative contribution of individual TFs to chromatin accessibility and explain how their function are combined to form active CREs.

Relevant publications:
Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation. Kreibich E,. et al. Molecular Cell. 2023.
Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding in vivo; Sönmezer, C, et al. Molecular Cell. 2021.
Studying transcription factor function in the genome at molecular resolution. Krebs, AR, Trends in Genetics. 2021.

ERC CoG investigator 2023.
Since January 2018 - Group leader at EMBL Genome Biology Unit.
Ambizione independent fellow at the FMI, Basel, Switzerland.
Postdoctoral research at the Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland. Advisor: Dirk Schübeler
PhD, 2011, IGBMC, Strasbourg, France. Advisor: Laszlo Tora
Masters in Molecular Biology (Uni Nancy, France) and Bioinformatics (Uni Pierre and Marie Curie, Paris).

Zoom link (with one-time registration for the whole series) for attending remotely: https://go.epfl.ch/EPFLBioETalks

Instructions for 1st-year Ph.D. students who are under EDBB’s mandatory seminar attendance rule:
IF you are not attending in-person in the room, please make sure to
  1. send D. Reinhard a note before noon on seminar day, informing that you plan to attend the talk online, and
  2. be signed in on Zoom with a recognizable user name (not a pseudonym making it difficult or impossible to be identified).
Students attending the seminar in-person should collect a confirmation signature after the talk - please print your own signature sheet beforehand (71 kB pdf available for download here).

Practical information

  • Informed public
  • Registration required