Chromatin phase separated nanoregions regulated by cross-linkers and explored by single particle trajectories

Abstract

Phase separated domains (PSDs) are ubiquitous in cell biology, representing nanoregions of high molecular concentration. PSDs appear at diverse cellular domains, such as neuronal synapses but also in eukaryotic cell nucleus, limiting the access of transcription factors and thus preventing gene expression. We study here the properties of PSDs and in particular how they can be generated by polymers. We show that increasing the number of cross-linkers generate a polymer condensation, preventing the access of diffusing molecules. To investigate how the PSDs restrict the motion of diffusing molecules, we estimate the mean residence and first escaping times. Finally, by computing the mean square displacement of single particle trajectories, we can reconstruct the properties of PSDs in term of a continuum range of anomalous exponents. To conclude, PSDs can result from a condensed chromatin, where the number of cross-linkers control the molecular access.