11-25 August 2019

Dr. Dusan Racko

Home Institution
Polymer Institute, Slovak Academy of Sciences, Dubravska cesta 3, 84541 Bratislava, Slovak Republic

Host Contact
Prof. Andrzej Stasiak

Host Institution
Center of Integrative Genomics, Building Genopode, 1015 Lausanne, Switzerland

Aim of the mission
The purpose of the STSM was to further test and develop our idea that the transcription induced supercoiling may be the driving force for the cohesin mediated loop extrusion essential for the TAD formation. From the previous works, we know supercoilig enhances contacts in contact maps, and we also know the supercoiling can exert mechanical work in terms of enthalpic pushing of cohesins. Now, we tested further the idea if much more loose supercoiling can also push cohesin rings by means of an entropic mechanism.

Summary of the results
We have developed a model for entropic loop extrusion in which the level of supercoiling was controlled by the friction between chromatin fibers and cohesin rings. We have shown that even low levels of supercoiling can drive loop extrusion. We have also shown in the entropic regime the loop can be extruded through both cohesin handcuff or a single ring embracing both fibers and loose supercoiling won’t produce anti-diagonal features on contact maps.

We are preparing a paper entitled “Entropic competition between supercoiled and relaxed portions of TADs is able to drive chromatin loop extrusion.”, and we prepared an abstract for a poster presentation for the Eutopia-2. The work carried out during the STSM opened new interesting questions and hopefully will lead to continuing collaborations on computer modelling of topological aspects that play biological role during gene expression and chromosome architecture.