Effective modeling of the chromatin structure by coarse-grained methods

Abstract

The interphase chromatin structure is extremely complex, precise and dynamic. Experimental methods can only show the frequency of interaction of the various parts of the chromatin. Therefore, it is extremely important to develop theoretical methods to predict the chromatin structure. In this publication, we implemented an extended version of the SBS model described by Barbieri et al. and created the ChroMC program that is easy to use and freely available (https://github.com/regulomics/chroMC) to other users. We also describe the necessary factors for the effective modeling of the chromatin structure in Drosophila melanogaster. We compared results of chromatin structure predictions using two methods: Monte Carlo and Molecular Dynamic. Our simulations suggest that incorporating black, non-reactive chromatin is necessary for successful prediction of chromatin structure, while the loop extrusion model with a long range attraction potential or Lennard-Jones (with local attraction force) as well as using Hi-C data as input are not essential for the basic structure reconstruction. We also proposed a new way to calculate the similarity of the properties of contact maps including the calculation of local similarity.

Communicated by Ramaswamy H. Sarma

Keywords:

• Chromatin
• chromatin structure
• modeling

Author contributions

All authors contributed to conceptualization of the study. PB wrote a prototype implementation of the ChroMC, IT improved the software, performed all experiments, analyzed the results and wrote the first version of the manuscript, that was then revised by BW and IT. All authors read and approved the final version of the manuscript.

Data availability statement

The code is available at https://github.com/regulomics/chroMC

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the National Science Centre grants [2014/15/N/NZ2/00397] and [2015/16/T/NZ2/00178] to PB and [2015/16/W/NZ2/00314] to BW and IT.