Multi-scale study of 3D Chromatin structure

Date: Monday 10 – Tuesday 11 April 2017

Venue: European Bioinformatics Institute (EMBL-EBI) – Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom

Application opens: Wednesday February 08 2017

Application deadline: Sunday March 19 2017

Participation: First come, first served

Contact: Frank O’Donnell

Registration fee: £80





This workshop will introduce delegates to a Virtual Research Environment (VRE), created by the Multi-scale complex Genomics project (MuG), to facilitate the analysis and interpretation of the genome. This environment integrates a range of data from genome annotation to 3D folding and DNA flexibility. Recent studies have shown the role that genome organisation can play in gene expression and the VRE has been designed to provide a way of analysing such data. This course will explore how to use the MuG VRE through two case studies; cohesin’s role in genome organisation in yeast and the proto-oncogene DNA-binding transcription factor Ets1. Both will show how to analyse chromatin structure, model DNA flexibility and protein-DNA interactions.


The workshop is aimed at both experimental (bench-based) researchers and bioinformaticians; additionally it may be of interest to tool developers who wish to integrate their tools into the VRE.

Participants should have an undergraduate understanding of biology AND have knowledge of genome organisation and the role it can play within the nucleus.

Syllabus, tools and resources

During this workshop you will learn about:

  • The Multi-scale complex Genomics project (MuG)
  • The MuG Virtual Research Environment (VRE)
  • Nucleosome dynamics
  • Hi-C, interaction matrices and TADs (topologically associating domains)
  • Protein-DNA interactions


After this workshop you will be able to:

Navigate the MuG VRE

  • Model and analyse a protein-DNA complex at the atomistic scale
  • Process Hi-C data sets to produce interaction matrices and TADs
  • Apply the MuG VRE to your own data sets


Time Topic Trainer
Day 1 – 10th April 2017
09:30 Registration and tea/coffee
09:50 – 10:00 Welcome to EMBL-EBI Andy Yates
10:00 – 10:30 MuG and participants Introduction Modesto Orozco
10:30 – 11:30

Presentation of Nucleosome Dynamics

Ricard Illa /Federica Battistini
11:30 – 12:00 Tea/coffee break
12:00 – 13:00 User case : Nucleosome dynamics at cohesin binding sites throughout the cell cycle in yeast Ricard Illa /Federica Battistini
13:00 – 14:00 Lunch
14:00 – 15:30

Coarse grained model of DNA; Build and analyze a sequence of interest.

Jürgen Walther
15:30 – 16:00 Tea/coffee break
16:00 – 17:00 Coarse grained model of Chromatin; Generation and analysis of chromatin fiber structures Jürgen Walther
17:15 Bus back to Cambridge Train Station
Day 2 – 11th April 2017
09:00 – 10:30 Presentation of Protein-DNA and protein-protein docking tools. Brian Jiménez
10:30 – 11:00 Tea/coffee break
11:00 – 12:30 Protein-DNA interactions, DNA flexibility and binding specificity. Marco Pasi / Federica Battistini
12:30 – 13:30 Lunch
13:30 – 15:00 Presentation of TADbit : Generation of Hi-C interaction matrices from Hi-C data François Serra
15:00 – 15:30 Tea/coffee break
15:30 – 17:00

Generation of populations of structures that satisfy the Hi-C interaction matrices and

Visualization of 3D models with TADkit

François Serra

17:00 – 17:30

Course wrap up and feedback Andy Yates
17:30 Course end