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Unraveling hierarchical chromatin dynamics and pioneer transcription factor interaction dynamics by smFRET

English title Unraveling hierarchical chromatin dynamics and pioneer transcription factor interaction dynamics by smFRET
Applicant Fierz Beat
Number 173169
Funding scheme Project funding (Div. I-III)
Research institution Institut des sciences et ingénierie chimiques EPFL - SB - ISIC
Institution of higher education EPF Lausanne - EPFL
Main discipline Biophysics
Start/End 01.07.2017 - 30.06.2021
Approved amount 700'000.00
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All Disciplines (3)

Discipline
Biophysics
Biochemistry
Physical Chemistry

Keywords (5)

Single-molecule FRET; Chromatin; Epigenetics; Dynamics; Pioneer transcription factor

Lay Summary (German)

Lead
Die menschliche Erbsubstanz (DNS) liegt im Zellkern als Komplex mit Verpackungsproteinen vor. Dieser Komplex wird Chromatin genannt. Chromatin ermöglicht eine definierte Ordnung der Chromosomen und spielt eine wichtige Rolle bei der Genregulation. Die Nahstruktur von Chromatin und deren Rolle bei der Genaktivierung ist jedoch nicht gut erforscht. Dieses Projekt hat zum Ziel Struktur und Dynamik von Chromatin aufzuklären.
Lay summary

Inhalt und Ziele des Forschungsprojekts

Chromatin ist massgeblich an der Organisation der DNS im eukaryotischen Zellker beteiligt. Chromatin besteht aus einer langen Kette von einzelnen Nukleosomen, der Grundeinheit von Chromatin. Diese Nukleosomenkette bildet eine Doppelhelixstruktur, die Chromatinfiber, welche grosse Teile der DNS für Zellprotein unerreichbar macht. Verschiedene molekulare Mechanismen existieren jedoch, welche diese Überstruktur verändern können, um damit Genexpression und andere Prozesse zu ermöglichen. Durch die schiere Grösse der Molekülstruktur von Chromatin sind die strukturellen und dynamischen Eigenschaften von Chromatinfibern nicht gut verstanden.

In unserem Projekt entwickeln wir Methoden um Chromatinfibern direkt zu beobachten und um die internen Strukturen und Bewegungen zu detektieren. Dazu benutzen wir Einzelmolekül Fluoreszenzmethoden, welche uns ermöglichen Chromatinfibern in hoher Raum- und Zeitauflösung zu vermessen. In einer ersten Phase des Projekts werden diese Methoden entwickelt, optimiert und in einer zweiten Phase angewandt um Chromatinfibern mit verschiedenem Aufbau zu charakterisieren.

In einer dritten Phase wenden wir die Methoden an um die Funktionsweise von Pioneer-Transkriptionsfaktoren zu verstehen. Dies sind Transkriptionsfaktoren, welche in kompaktes Chromatin eindringen können um Gene zu aktivieren. Dieser Teil des Projekts wird in Kollaboration mit Prof. David Shore (Universität Genf) durchgeführt.

Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts

Das Projekt befasst sich mit Grundlagenforschung. Um Chromatinstruktur, Dynamik und Funktion zu verstehen ist ein interdisziplineller Ansatz zwischen Biologie, Chemie und Biophysik nötig. Die errungenen Einsichten sind fundamentaler Natur und können unser Bild von unserer Erbstubstanz massgeblich verändern, mit Implikationen für unser Verständnis von organismischer Entwicklung, der Biologie von Stammzellen oder der Entstehung von Krebs.

Direct link to Lay Summary Last update: 19.05.2017

Responsible applicant and co-applicants

Employees

Project partner

Publications

Publication
Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor
Mivelaz Maxime, Cao Anne-Marinette, Kubik Slawomir, Zencir Sevil, Hovius Ruud, Boichenko Iuliia, Stachowicz Anna Maria, Kurat Christoph F., Shore David, Fierz Beat (2020), Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor, in Molecular Cell, 77(3), 488-500.e9.
Observing protein interaction dynamics to chemically defined chromatin fibers by colocalization single-molecule fluorescence microscopy
Mivelaz Maxime, Fierz Beat (2020), Observing protein interaction dynamics to chemically defined chromatin fibers by colocalization single-molecule fluorescence microscopy, in Methods.
Chemical and biophysical methods to explore dynamic mechanisms of chromatin silencing
Boichenko Iuliia, Fierz Beat (2019), Chemical and biophysical methods to explore dynamic mechanisms of chromatin silencing, in Current Opinion in Chemical Biology, 51, 1-10.
Biophysics of Chromatin Dynamics
Fierz Beat, Poirier Michael G. (2019), Biophysics of Chromatin Dynamics, in Annual Review of Biophysics, 48(1), 321-345.
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α
Kilic Sinan, Felekyan Suren, Doroshenko Olga, Boichenko Iuliia, Dimura Mykola, Vardanyan Hayk, Bryan Louise C., Arya Gaurav, Seidel Claus A. M., Fierz Beat (2018), Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α, in Nature Communications, 9(1), 235-235.
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage
Kilic Sinan, Boichenko Iuliia, Lechner Carolin C., Fierz Beat (2018), A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage, in Chemical Science, 9(15), 3704-3709.

Datasets

Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor\_FigureS6

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.3270526
Repository Zenodo


Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor\_Figure5f\_1

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.3269904
Repository Zenodo


Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor\_Figure5e\_2

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.3269880
Repository Zenodo


Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor\_Figure5e\_1

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.3269823
Repository Zenodo


Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor\_Figure5f\_2

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.3270478
Repository Zenodo


Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor\_Fig.2,3,S3,S4,S7

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.3260205
Repository Zenodo


A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4e

Author Kilic, Sinan; Boichenko, Iuliia; Lechner, Carolin C.; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.1477026
Repository Zenodo


A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4d

Author Kilic, Sinan; Boichenko, Iuliia; Lechner, Carolin C.; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.1477022
Repository Zenodo


A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4f

Author Kilic, Sinan; Boichenko, Iuliia; Lechner, Carolin C.; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.1477024
Repository Zenodo


Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 1df

Author Kilic, Sinan; Felekyan, Suren; Doroshenko, Olga; Boichenko, Iuliia; Dimura, Mykola; Vardanyan, Hayk; Bryan, Louise C.; Arya, Gaurav; Seidel, Claus.A.M.; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.1040772
Repository Zenodo


Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 7cde

Author Kilic, Sinan; Felekyan, Suren; Doroshenko, Olga; Boichenko, Iuliia; Dimura, Mykola; Vardanyan, Hayk; Bryan, Louise C.; Arya, Gaurav; Seidel, Claus.A.M.; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.1069677
Repository Zenodo


Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 2def

Author Kilic, Sinan; Felekyan, Suren; Doroshenko, Olga; Boichenko, Iuliia; Dimura, Mykola; Vardanyan, Hayk; Bryan, Louise C.; Arya, Gaurav; Seidel, Claus A.M.; Fierz, Beat
Persistent Identifier (PID) 10.5281/zenodo.1069675
Repository Zenodo


GEO Series GSE134143

Author Mivelaz, Maxime; Cao, Anne-Marinette; Kubik, Slawomir; Zencir, Sevil; Hovius, Ruud; Boichenko, Iuliia; Stachowicz, Anna Maria; Kurat, Christoph F.; Shore, David; Fierz, Beat
Persistent Identifier (PID) GSE134143
Repository GEO


Collaboration

Group / person Country
Types of collaboration
David Suter, EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Nicolas Thomä, FMI Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Andrea Ablasser, EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
4th Chemical Ligation Meeting Talk given at a conference Synthetic and single-molecule exploration of the dynamic chromatin landscape »  27.01.2020 Orléans, France Fierz Beat;
International Symposium on Chemical Biology Poster Multivalent peptide probes for chromatin states investigation 22.01.2020 Geneva, Switzerland Guidotti Nora;
International Symposium on Chemical Biology Poster Shaping the centromere – role of CCAN proteins in determining centromere chromatin 22.01.2020 Geneva, Switzerland Nagpal Harsh;
Dynamic Chromatin Binding and Remodelling Mechanism of Pioneer Transcription Factors Poster Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor 22.01.2020 Geneva, Switzerland Mivelaz Maxime Nicolas;
UNIL CIG Seminar Individual talk Gene control with a "twist" : Exploring the dynamic chromatin landscape 21.10.2019 Lausanne, Switzerland Fierz Beat;
Seminar University of Basel Individual talk Gene control with a "twist" : Exploring the dynamic chromatin landscape 04.10.2019 Basel, Switzerland Fierz Beat;
FEBS Workshop on Chromatin Proteomics 2019 Talk given at a conference Synthetic and single-molecule exploration of the dynamic chromatin landscape 23.09.2019 Heraklion, Greece Fierz Beat;
EBSA 2019 Talk given at a conference Gene control with a "twist" : Exploring the dynamic chromatin landscape 21.07.2019 Madrid, Spain Fierz Beat;
Seminar - DKFZ Heidelberg Individual talk Revealing dynamic invasion by pioneer transcription factors on the single-molecule scale 02.07.2019 Heidelberg, Germany Fierz Beat;
Chemical Protein Synthesis Meeting 2019 Poster Multivalent peptide probes for chromatin states investigation 16.06.2019 Berlin, Germany Guidotti Nora;
Albany 2019 : 20th conversation Talk given at a conference Revealing dynamic invasion mechanisms of pioneer transcription factors into compact chromatin 11.06.2019 Albany, United States of America Fierz Beat;
Seminar - University of Dundee Individual talk Gene control with a "twist" :Using chemistry to explore the dynamic chromatin landscape 09.05.2019 Dundee, Great Britain and Northern Ireland Fierz Beat;
ABCAM Chromatin and Epigenetics: Inheritance and Design Talk given at a conference Probing the dynamic interaction landscape of modified chromatin 01.04.2019 Munich, Germany Fierz Beat;
EpiChrom2019 Talk given at a conference Revealing the mechanistic basis of chromatin invasion by pioneer transcription factors 15.02.2019 Stockholm, Sweden Fierz Beat;
Seminar - Institut Curie Individual talk Gene control with a "twist" : Exploring the dynamic chromatin landscape 12.02.2019 Paris, France Fierz Beat;
CHAINS 2018 – Chemistry as Innovating Science Talk given at a conference Revealing transcription factor invation into compact chromatin 03.12.2018 Veldhoven, Netherlands Fierz Beat;
LS2 meeting : Quantitative Network Biology Talk given at a conference Probing dynamic chromatin organization on the single-molecule scale 19.11.2018 Kandersteg, Switzerland Fierz Beat;
Swiss chemical society fall meeting Poster Shaping the centromere – role of CCAN proteins in determining centromere chromatin 07.09.2018 Lausanne, Switzerland Nagpal Harsh;
EMBO Workshop in Chemical Biology Talk given at a conference Dynamic chromatin regulation on the single-molecule scale 29.08.2018 Heidelbeg, Germany Fierz Beat;
Swiss chemical biology summer school 2018 Poster Shaping the centromere – role of CCAN proteins in determining centromere chromatin 19.08.2018 Villars-sur-Ollon, Switzerland Nagpal Harsh;
Summer School in Chemical Biology Poster Multivalent peptide probes for chromatin states investigation 19.08.2018 Villars-sur-Ollon, Switzerland Guidotti Nora;
Chromatin Structure and Function - Gordon Research Conference Talk given at a conference Dynamic transcription factor access to compact chromatin 23.07.2018 Newry, Maine, United States of America Fierz Beat;
Seminar MIT Individual talk Synthetic and single-molecule approaches to reveal dynamic chromatin regulation 20.07.2018 Cambridge, USA, United States of America Fierz Beat;
Special Seminar - Harvard Individual talk Synthetic and single-molecule approaches to reveal dynamic chromatin regulation 19.07.2018 Harvard, United States of America Fierz Beat;
Seminar University of Basel Individual talk Synthetic and single-molecule approaches to reveal dynamic chromatin regulation 28.05.2018 Basel, Switzerland Fierz Beat;
Retreat 2018 of the Molecular Biosciences at the University of Bayreuth Talk given at a conference Synthetic and single-molecule approaches to reveal dynamic chromatin regulation 03.05.2018 Lichtenfels, Germany Fierz Beat;
UCSD Seminar Individual talk Synthetic and single-molecule approaches to reveal dynamic chromatin regulation 25.04.2018 San Diego, United States of America Fierz Beat;
Seminar The SCRIPPS Research Institute Individual talk Synthetic and single-molecule approaches to reveal dynamic chromatin regulation 24.04.2018 La Jolla, CA, United States of America Fierz Beat;
ASBMB Annual Meeting 2018 Talk given at a conference Revealing chromatin state organization on the single-molecule scale 22.04.2018 San Diego, United States of America Fierz Beat;
van Leeuwenhoek Lecture on BioScience Individual talk Revealing chromatin state organization on the single-molecule scale 19.04.2018 Leiden, Netherlands Fierz Beat;
Biophysical Society 62nd Annual Meeting New and Notable Symposium Talk given at a conference The dynamic organisation of modified chromatin fibers revealed by smFRET 21.02.2018 San Francisco, United States of America Fierz Beat;
CECAM - Lorenz joint Workshop Talk given at a conference A single-molecule view of the dynamic organization of modified chromatin fibers 19.01.2018 Lausanne, Switzerland Fierz Beat;
NCCR Chemical Biology Symposium Poster Dynamic Chromatin Binding and Remodelling Mechanism of Pioneer Transcription Factors 10.01.2018 Geneva, Switzerland Mivelaz Maxime Nicolas;
International Symposium on Chemical Biology Poster Controlling the supramolecular assembly of nucleosomes asymmetrically modified on H4 10.01.2018 Geneva, Switzerland Guidotti Nora;
4th International Symposium of the Collaborative Research Center 765 Talk given at a conference Revealing chromatin state organization on the single-molecule scale 03.10.2017 Berlin, Germany Fierz Beat;
GBM Fall Conference – The Molecular Basis of Life, Ruhr-University Bochum Talk given at a conference A single-molecule view on heterochromatin dynamics 25.09.2017 Bochum, Germany Fierz Beat;
The 7th CPS Meeting Talk given at a conference Probing the multivalent readout of chromatin modification patterns 04.09.2017 Haifa, Israel Fierz Beat;
EMBO Conference The Nucleosome: From Atoms to Genomes Talk given at a conference Multiscale structural dynamics in chromatin fibers revealed by single-molecule FRET 30.08.2017 Heidelberg, Germany Fierz Beat;
EPFL-KAIST Symposium Talk given at a conference Revealing chromatin state organization on the single-molecule scale 28.08.2017 Daejon, Korean Republic (South Korea) Fierz Beat;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Déguiser l’ADN en guirlande lumineuse pour mieux l’étudier Avenir et Sciences International 2019

Awards

Title Year
New & Notable Symposium of the 62nd Biophysical Society Annual Symposium 2018 2018

Associated projects

Number Title Start Funding scheme
149789 Chromatin: A Dynamic Platform for Protein-Protein Interactions 01.02.2014 Project funding (Div. I-III)

Abstract

The structure and internal motions of chromatin are a determining factor in all chromatin transactions, including gene activation, transcription, DNA replication or DNA repair. Thus a deep understanding of the molecular organization of chromatin is of great importance. Chromatin structure and function is regulated by the incorporation of histone variants, modifications of the DNA and, in particular, post-translational modifications (PTMs) of the histones, in combination with protein effectors. Studies using X-ray and electron microscopy approaches revealed that chromatin fibers are organized in stacks of compact tetranucleosome units. However, as a whole, chromatin structure and dynamics are still enigmatic as it is a conformationally and chemically heterogeneous and highly dynamic complex. Hence, new approaches are required.A key process governed by local chromatin organization and conformational dynamics is gene regulation through transcription factors. Repressed genes reside in a compact chromatin compartment, heterochromatin, with restricted biochemical accessibility. A first step to activate such genes, e.g. during development, requires an initial, or pioneer transcription factor (pTF) to access target sites in compact chromatin. Such pTFs have the ability to invade compact chromatin, remodel its structure and initiate the assembly of further factors to subsequently enact a change in the chromatin state (i.e. the presence of histone variants, PTMs, the positioning of nucleosomes). We hypothesize that the ability of pTFs to bind target sites on nucleosomes, combined with the transient exposure of such sites due to conformational fluctuations in compact chromatin, enables their pioneering activity. When bound, pTFs then enact dynamic opening of the structure allowing gene transcription to take place. How pTFs can bypass chromatin inhibition and then remodel the structure is not well understood and a major current biological question.Here, we will elucidate dynamic chromatin structure and the molecular basis of pTF function using a novel combination of single-molecule and chemical biology approaches. In recent years, we have developed a suite of chemical and biophysical methods to mechanistically probe chromatin regulatory processes in highly defined systems with single-molecule resolution. We are thus uniquely positioned to investigate fundamental chromatin processes at unprecedented spatiotemporal resolution, and answer the following questions:1. What is the dynamic organization of chromatin fibers? Here we will implement a single-molecule fluorescence resonance energy transfer (smFRET) approach to directly determine local chromatin structure and dynamics as a function of nucleosome positioning and fiber architecture.2. Which interactions govern local dynamics in chromatin arrays? Key contacts between nucleosomes are modulated by histone variants and PTMs. We will use our smFRET approach to reveal how chromatin structure is dynamically remodeled by these modifications, enabling TF access to internal sites.3. How do pioneer TFs access target sites in compact chromatin? Using the yeast pTF Rap1 as a model, we will gain mechanistic insight into pTF action in compact chromatin fiber of defined architecture.Taken together, these studies will provide, for the first time, direct insight into the conformational heterogeneity, dynamics and energetics of chromatin fibers, and how they are accessed by pTFs. We are convinced that our methods will pave the way to a molecular understanding of chromatin regulation.
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