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Chromatin: A Dynamic Platform for Protein-Protein Interactions

English title Chromatin: A Dynamic Platform for Protein-Protein Interactions
Applicant Fierz Beat
Number 149789
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 01.02.2014 - 31.01.2017
Approved amount 382'000.00
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All Disciplines (4)

Discipline
Biophysics
Biochemistry
Organic Chemistry
Molecular Biology

Keywords (6)

DNA damage repair; Chromatin; Chromatin remodeling; Epigenetics; Protein chemistry; Biophysics

Lay Summary (German)

Lead
Im eukaryotischen Zellkern ist die DNS als Chromatin organisiert, bestehend aus Nukleosomen, Spulen von Histon-Proteinen und, darum gewickelt, genomischer DNS. Die Aktivität von Genen auf der DNS wird von chemischen Modifikationen der Histon-Proteine beeinflusst. Die Modifikationen werden von spezifischen Bindungs-Proteinen erkannt, welche dann am Chromatin verankert (rekrutiert) werden. Dadurch verändert sich die Chromatin Struktur und Umgebung, und Gene werden an- oder abgeschaltet. Dies führt zu Zelldifferenzierung und Organismenbildung, oder, im Falle von Fehlregulation, zu Erkrankungen wie Krebs.
Lay summary

Inhalt und Ziel des Forschungsprojekts

Wir benutzen Peptid- und Proteinchemie um modifizierte Chromatinstränge künstlich herzustellen. Die Eigenschaften und Funktionsweise von solch exakt defininertem Chromatin kann dann mittels Biophysikalischen Methoden genau untersucht werden. In diesem Projekt etablieren wir eine Einzelmolekül-Methode die uns ermöglicht die dynamischen Interaktionen von Bindungsproteinen mit modifizeren Chromatin Strängen zu messen. Wir werden uns auf die Aufklärung der dynamischen Chromatin-Interaktionen von zwei Bindungsproteins-Klassen konzentrieren: Proteine, involviert in der Reparatur von DNS Schäden (z.B. 53BP1) und Proteine, welche Nukleosomen gezielt verschieben und dadurch Gen-Expression beeinflussen (Remodeling Enzymes, z.B. ACF). Wir erwarten aus diesen Experiementen fundamentale Erkenntnisse über die Funktion von Histon-Modifikationen zu erlangen, nämlich wie sie mit Bindungsproteinen interagieren und diese zum Chromatin rekrutieren.

Wissenschaftlicher und gesellschaftlicher Kontext der Forschungsprojekte

Die obengenannten Arbeiten haben medizinische Relevanz, da Chromatin-Bindungsproteine zunehmend als geeignete Therapie-Ziele für Krebserkrankungen identifiziert werden. Zudem tragen unsere Untersuchungen zum quantitativen Verständnis fundamentaler Mechanismen in der Biologie bei.

Direct link to Lay Summary Last update: 27.01.2014

Responsible applicant and co-applicants

Employees

Publications

Publication
Dynamic Chromatin Regulation from a Single Molecule Perspective
Fierz Beat (2016), Dynamic Chromatin Regulation from a Single Molecule Perspective, in ACS CHEMICAL BIOLOGY, 11(3), 609-620.
Multivalency governs HP1 alpha association dynamics with the silent chromatin state
Kilic Sinan, Bachmann Andreas L., Bryan Louise C., Fierz Beat (2015), Multivalency governs HP1 alpha association dynamics with the silent chromatin state, in NATURE COMMUNICATIONS, 6, 7313.

Collaboration

Group / person Country
Types of collaboration
Suliana Manley Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Vassily Hatzimanikatis 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
PSL* Chemical Biology Symposium Poster Chromatin structure and DNA interactions control HP1 dynamics 08.12.2016 Paris, France Bryan Louise;
MPI Biochemistry, München, Seminar Series Talk given at a conference Probing the function of histone PTMs - one molecule at a time 11.08.2016 Munich, Germany Fierz Beat;
Chemical biology lecture series, University Dortmund Individual talk Probing the function of histone PTMs - one molecule at a time 28.06.2016 Dortmund, Germany Fierz Beat;
Epigeneswiss conference Talk given at a conference Probing the function of histone PTMs - one molecule at a time 07.06.2016 Weggis, Switzerland Bryan Louise; Fierz Beat;
Gordon conference, Chromatin Structure & Function Talk given at a conference Probing the function of histone PTMs - one molecule at a time 25.05.2016 Les Diablerets, Switzerland Fierz Beat;
University of Copenhagen, Copenhagen, Seminar series Individual talk Probing the molecular function of histone modifications - one molecule at a time 12.05.2016 Copenhagen, Denmark Fierz Beat;
UCSF Chromatin club lecture series, UC San Francisco Individual talk Probing the molecular function of histone modifications - one molecule at a time 29.02.2016 San Francisco, United States of America Fierz Beat;
Gordon conference, Chemistry & Biology of Peptides Talk given at a conference Probing the molecular function of histone modifications - one molecule at a time 25.02.2016 Ventura, United States of America Fierz Beat;
Kelley lectureship MBS lecture series, UT Austin Talk given at a conference Probing the molecular function of histone modifications - one molecule at a time 19.02.2016 Austin, United States of America Fierz Beat;
DKFZ Seminar series, DKFZ Heidelberg Talk given at a conference Probing the molecular function of histone modifications - one molecule at a time 11.02.2016 Heidelberg, Germany Fierz Beat;
EMBL Grenoble, Grenoble, France, Seminar series Individual talk Probing the molecular function of histone modifications - one molecule at a time 18.01.2016 Konstanz, Germany Fierz Beat;
Konstanz Research School - Chemical Biology Seminar Individual talk Probing the molecular function of histone modifications - one molecule at a time 20.10.2015 Konstanz, Germany Fierz Beat;
59th Biophysical society meeting Talk given at a conference Heterochromatin dynamics on the single molecule level 02.10.2015 Baltimore, United States of America Fierz Beat;
14th Conference on Methods and Applications of Fluorescence Talk given at a conference Dissecting epigenetic signaling on the single-molecule scale 14.09.2015 Würzburg, Germany Fierz Beat;
Curie Institute, Seminar series Individual talk Probing the molecular function of histone modifications - one molecule at a time 10.09.2015 Paris, France Fierz Beat;
Biochemical Institute, University Zürich, Lecture series Individual talk Probing chromatin function through chemistry 13.08.2015 Zürich, Switzerland Fierz Beat;
10th European Biophysics Congress Talk given at a conference Single molecule epigenetics: HP1 recruitment dynamics 20.07.2015 Dresden, Germany Fierz Beat;
ISACS 16, Challenges in Chemical Biology 2015 Talk given at a conference Single molecule epigenetics: HP1 recruitment dynamics 17.06.2015 Zürich, Switzerland Fierz Beat;
Le Mazelet meeting on chromosome biology 2014 Talk given at a conference Heterochromatin dynamics on the single molecule level 03.11.2014 Montpellier, France Fierz Beat;
11th EMBL Conference: Transcription and Chromatin Talk given at a conference Heterochromatin dynamics on the single molecule level 24.08.2014 Heidelberg, Germany Fierz Beat;


Self-organised

Title Date Place
Summer school on “Molecular and chemical mechanisms in epigenetics” 14.07.2015 Arolla, Switzerland
Chromatin Winter School 02.05.2014 Crans Montana, Switzerland

Associated projects

Number Title Start Funding scheme
173169 Unraveling hierarchical chromatin dynamics and pioneer transcription factor interaction dynamics by smFRET 01.07.2017 Project funding (Div. I-III)

Abstract

Post-translational modifications (PTMs) of histone proteins play a crucial role in regulating chromatin function. Effector proteins involved in DNA remodeling and DNA damage repair (e.g. the DNA damage signaling protein 53BP1 or the chromatin remodeler ACF) interact with patterns of histone PTMs through specific protein-protein interaction domains (reader domains). Through histone PTM - reader domain interactions, the effectors are dynamically recruited from a soluble and freely dif-fusible pool and translate to chromatin regions in the nucleus where their activity is required. It is currently not well understood how relatively low-affinity interactions between histone PTMs and effector reader domains (with dissociation constants in the range of 5-100 micromolar) result in a specific spatial arrangement of effector complexes, often rapidly as a result of an altered chromatin state.To shed light on these recruitment processes, we are quantitatively investigating the molecular mechanism of dynamic protein localization through histone PTMs. To this end, we are developing a defined in vitro system which allows to measure the complex binding kinetics of 53PB1 and ACF to chromatin fibers carrying varying concentrations of their cognate histone marks.Employing chemical protein semisynthesis and DNA engineering we construct chromatin fibers of a distinct architecture and carrying a defined set of histone PTMs. We are then using a combination of fluorescence correlation spectroscopy and single-molecule total internal reflection fluorescence (TIRF) microscopy to determine effector binding constants and dwell times dependent on the chromatin modification status, chromatin conformation, effector interactions and solvent conditions.Quantitative analysis of dynamic chromatin processes in vitro is required to gain a better understanding of these processes in the more complex environment of a nucleus. We thus expect that our analyses will significantly advance our knowledge of key aspects of the molecular mechanisms at work in histone PTM mediated effector recruitment in chromatin remodeling and DNA repair.
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