CECAM

CECAM-Lorentz Joint Workshop: Multiscale-modelling of nucleosomes and their positioning on DNA

Location : CECAM-HQ-EPFL, Lausanne, Switzerland
January 15, 2018 – January 19, 2018

Conference now full due to space limitations and we are no longer able to accept further participants unless there are cancellations. Please still apply and we will add you to a waiting list.

About three quarters of our DNA is wrapped around protein cylinders forming nucleosomes. The location of nucleosome binding is known to be biologically crucial, e.g. to be closely connected to epigenetics via methylation patterns. As the DNA is strongly bent in a nucleosome the affinity of a given stretch of DNA depends on its elasticity and shape as encoded in its letters, i.e. the nucleotide sequence as well as on methylation patterns and other base modifications. (This is unlike in a book where the text that is printed does not affect the elasticity of the paper.) In addition, mechanical cues can also be written on top of genes exploiting the fact that the genetic code is degenerate. This suggests that DNA molecules have evolved mechanically to guide their own packaging on nucleosomes which in turn affects the expression of their genes.

To understand the role of sequence-dependent DNA elasticity in gene expression requires the coordinated effort of many different theoretical and simulation groups with expertise ranging from all-atom molecular dynamics simulations of DNA, building of coarse-grained mathematical models of DNA and nucleosomes up to bioinformatics approaches that study properties of whole genomes, as well as of course actual experimentalists. This is the right time to set such a concerted effort in motion as high quality data are pouring in almost daily ranging from single-molecule experiments up to genome-wide nucleosome cartography for many organisms.

Belgium

Bernardo Oyarzun (Universite Libre de Bruxelles)

France

Benjamin Audit (invited speaker) (CNRS – ENS de Lyon)
Ralf Blossey (invited speaker) (CNRS UGSF 8576)
Nicolas Destainville (invited speaker) (University Paul Sabatier, Toulouse)
Ralf Everaers (invited speaker) (École Normale Supérieure de Lyon)
Richard Lavery (invited speaker) (CNRS – Institute of Biology and Chemistry of Proteins (IBCP), Lyon)
Cedric Vaillant (invited speaker) (Laboratoire de Physique, ENS Lyon)

Germany

Wenping Lyu (RWTH Aachen University)

Ireland

Andrew Flaus (National University of Ireland)

Italy

Diego Liberati (Consiglio Nazionale delle Ricerche)

Japan

Giovanni Brandani (invited speaker) (Kyoto University)

Lithuania

Daiva Petkeviciute (Kaunas University of Technology, Lithuania)

The Netherlands

Lennart De Bruin (Lorentz Institute, Leiden University)
Behrouz Eslami Mossallam (Bionanoscience department, TU Delft)
Ignacio Faustino
Jonas Neipel (Leiden University)
Bahareh Shakiba (Lorentz Institute, Leiden University)
John van Noort (invited speaker) (LION, Leiden University)
Renger Zoonen (Leiden University)
Martijn Zuiddam (Leiden University)

Singapore

Vishal Minhas (NTU)

Spain

Federica battistini (IRB BARCELONA)
Pablo Dans Puiggròs (IRB Barcelona)
Modesto Orozco (invited speaker) (University of Barcelona and Institute for Research in Biomedicine)
Jürgen Walther (IRB Barcelona)

Switzerland

Beat Fierz (invited speaker) (Swiss Federal Institute of Technology, Lausanne)
Pétur Heidarsson (University of Zurich)
Alessandro Patelli (EPFL)
Ben Schuler (invited speaker) (University of Zurich)
Thibaud von Erlach (Swiss Federal Institute of Technology, Lausanne (EPFL))
Thomas Zwahlen (EPFL)

Tunisia

Nadia chouaieb (ecole nationale d ingenieurs de tunis)

United Kingdom

Vladimir Teif (invited speaker) (University of Essex)

USA

Alexei Aksimentiev (invited speaker) (University of Illinois at Urbana-Champaign)
Craig John Benham (invited speaker) (Dept of Mathematics, UC Davis)
Juan J de Pablo (invited speaker) (University of Chicago)
Taekjip Ha (invited speaker) (Dept of Biomedical Engineering, Johns Hopkins, Baltimore)
Alexandre V. Morozov (invited speaker) (Rutgers University)
Wilma Olson (invited speaker) (Rutgers University)
Lois Pollack (invited speaker) (Cornell University)
Andrew J. Spakowitz (invited speaker) (Stanford University)
Jeff Wereszczynski (Illinois Institute of Technology)
Victor Zhurkin (invited speaker) (National Cancer Institute, NIH )

Monday January 15th 2018 – Day 1
 

09:00 to 10:00 – Registration
10:00 to 11:00 – Alexei Aksimentiev 
Molecular Dynamics Adventures with DNA
11:00 to 11:30 – Coffee Break
11:30 to 12:30 – Nicolas Destainville 
What is the energy required to pinch a DNA plectoneme?
12:30 to 14:30 – Lunch
14:30 to 15:30 – Andrew J. Spakowitz 
Physical Modeling of Chromosomal Organization and Epigenetic Regulation
15:30 to 16:30 – Ben Schuler 
A biological polyelectrolyte complex in histone H1 chaperoning
16:30 to 19:30 – Poster Session with cold buffet sandwiches
Tuesday January 16th 2018 – Day 2
 

09:00 to 10:00 – Lois Pollack 
DNA release from histones in nucleosome core particles: measurements and models
10:00 to 11:00 – Ralf Everaers 
Histone-DNA interaction potentials from high-resolution structures of the nucleosome
11:00 to 11:30 – Coffee Break
11:30 to 12:30 – Juan J de Pablo 
A multiscale representation of DNA-histone structure and dynamics
12:30 to 14:00 – Lunch
14:00 to 15:00 – Wilma Olson 
Nucleosome positioning and composition influence long-distance communication in model chromatin systems
15:00 to 15:30 – Alessandro Patelli 
cgDNA+: a coarse grain model of DNA with explicit treatment of the phosphate groups
15:30 to 16:00 – Thomas Zwahlen 
Genome-scale scanning with the cgDNA statistical mechanical model
16:00 to 16:30 – Coffee Break
16:30 to 17:00 – Martijn Zuiddam 
The physics behind the mechanical nucleosome positioning code
17:00 to 17:30 – Lennart De Bruin 
In silico unwrapping of designer nucleosomes
Wednesday January 17th 2018 – Day 3
 

09:00 to 10:00 – Alexandre V. Morozov 
Statistical Mechanics of Nucleosomal Arrays
10:00 to 11:00 – Craig John Benham 
Competitive Transitions in Superhelical DNA
11:00 to 11:30 – Coffee Break
11:30 to 12:30 – Giovanni Brandani 
Coarse-grained MD simulations of passive and active nucleosome sliding via twist defects
12:30 to 15:00 – Lunch
15:00 to 16:00 – Vladimir Teif 
Interplay of epigenetic modifications and nucleosome positioning
16:00 to 16:30 – Coffee Break
16:30 to 17:30 – Ralf Blossey 
Molecular motor models of chromatin remodelers
19:30 to 22:00 – Social Dinner
Thursday January 18th 2018 – Day 4
 

09:00 to 10:00 – Taekjip Ha 
DNA physics and chromatin function
10:00 to 11:00 – Richard Lavery 
Nucleosome Perturbations: Remodelling intermediates and H1 Binding
11:00 to 11:30 – Coffee Break
11:30 to 12:30 – Cedric Vaillant 
Epigenomics in 3D: modeling the dynamic coupling between epigenome and chromatin organization
12:30 to 15:00 – Lunch
15:00 to 16:00 – Victor Zhurkin 
Topological polymorphism of chromatin fibers. (DNA linking number; transcription; epigenetic landscape)
16:00 to 16:30 – Coffee Break
16:30 to 17:30 – John van Noort 
The structure of chromatin; single-molecule experiments on model fibers and real gene
Friday January 19th 2018 – Day 5
 

09:00 to 10:00 – Modesto Orozco 
Understanding nucleosome fiber in chromatin
10:00 to 11:00 – Beat Fierz 
A single-molecule view of the dynamic organization of modified chromatin fibers
11:00 to 11:30 – Coffee Break
11:30 to 12:30 – Benjamin Audit 
Universal Sequence Encoding of an Accessible Nucleosomal Chromatin Fiber across Vertebrates