Modeling chromosomes: Beyond pretty pictures

Maxim V Imakaev; Geoffrey Fudenberg; Leonid A Mirny

doi:10.1016/j.febslet.2015.09.004

Modeling chromosomes: Beyond pretty pictures

FEBS Lett. 2015 Oct 7;589(20 Pt A):3031-6. doi: 10.1016/j.febslet.2015.09.004. Epub 2015 Sep 10.

Authors

Maxim V Imakaev¹, Geoffrey Fudenberg², Leonid A Mirny³

Affiliations

¹ Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
² Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
³ Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Abstract

Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data-driven ensembles, and two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address.

Keywords: Chromatin; Hi-C; Model; Polymer; Simulation.

Publication types

Research Support, N.I.H., Extramural
Review

MeSH terms

Animals
Chromatin / physiology
Chromatin / ultrastructure*
Chromosome Mapping
Computer Simulation
Humans
Models, Molecular

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding