Dynamics as a cause for the nanoscale organization of the genome. Issue 1 (1st January 2020)

• Record Type: Journal Article
• Authors: Barth, Roman; Fourel, Genevieve; Shaban, Haitham A.
• Is Part Of: Nucleus. Volume 11: Issue 1(2020)
• Page Start: 83
• Page End: 98
• Publication Date: 2020-01-01
• Subjects: Genome organization -- Chromatin dynamics -- 4D genome -- Deep-PALM -- Granger-causality -- Active polymers; Cell nuclei -- Periodicals; Biology -- Periodicals; Biology; Cell nuclei; Periodicals; 571.6605
• DOI: 10.1080/19491034.2020.1763093
• Languages: English
• ISSNs: 1949-1034

Abstract

ABSTRACT: Chromatin 'blobs' were recently identified by live super-resolution imaging of labeled nucleosomes as pervasive but fleeting structural entities. However, the mechanisms leading to the formation of these blobs and their functional implications are unknown. We explore here whether causal relationships exist between parameters that characterize the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant for both blob area and local density. Such causality, however, could be demonstrated only in 10–20% of the nucleus, suggesting that chromatin dynamics and structure at the nanometer scale are dominated by stochasticity. We show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Our results represent a first step toward elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in the cell nucleus.