Genome organization in the nucleus: From dynamic measurements to a functional model

Abstract

A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed. The structure and function of a biological system are closely related to its dynamic properties, thus further emphasizing the importance of identifying the rules governing the dynamics that cannot be directly deduced from information on the structure itself. In eukaryotic cells, tens of thousands of genes are packed in the small volume of the nucleus. The genome itself is organized in chromosomes that occupy specific volumes referred to as chromosome territories. This organization is preserved throughout the cell cycle, even though there are no sub-compartments in the nucleus itself. This organization, which is still not fully understood, is crucial for a large number of cellular functions such as gene regulation, DNA breakage repair and error-free cell division. Various techniques are in use today, including imaging, live cell imaging and molecular methods such as chromosome conformation capture (3C) methods to better understand these mechanisms. Live cell imaging methods are becoming well established. These include methods such as Single Particle Tracking (SPT), Continuous Photobleaching (CP), Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS) that are currently used for studying proteins, RNA, DNA, gene loci and nuclear bodies. They provide crucial information on its mobility, reorganization, interactions and binding properties. Here we describe how these dynamic methods can be used to gather information on genome organization, its stabilization mechanisms and the proteins that take part in it.

Chromatin dynamics governed by a set of nuclear structural proteins

“…We monitor the dynamics of different genomic sites in the nucleus, and by thoroughly analyzing the dynamics, we can extract relevant information about the structure, organization, and function. 63 More specifically, we mainly use two methods. In the first, we label telomeres, centromeres, or any genetic site in live cells and follow their motion in time by single-particle tracking (SPT).…”

“…During the last few years, we developed a methodology for studying the organization of the genome in the nucleus by using live cell imaging. We monitor the dynamics of different genomic sites in the nucleus, and by thoroughly analyzing the dynamics, we can extract relevant information about the structure, organization, and function . More specifically, we mainly use two methods.…”

In vivo, chromatin is a fluctuating polymer chain at equilibrium constrained by internal friction

“…For instance, the recurrent detection of irregular 10-nm fibers by cryo-TEM of thin nuclear sections is questioning the relevance of solenoid or helicoid models of nucleosome arrays (6)(7)(8). This problem has not been clarified by probing the motion of chromosomes in vivo, although dynamic measurements offer a unique opportunity to infer structural properties of genome organization (9). Indeed, we and others have shown that chromosome dynamics in yeast is characterized by sub-diffusive behavior detected by a non-linear temporal variation of the mean square displacement (MSD) of chromosome loci (10)(11)(12)(13)(14)(15)(16):…”

The Energy as a Determinant Factor in the Ethiopathogeny of Chromosomal Abnormalities. The Unsuspected Bioenergetic Role of Melanin

“…The interaction of chromatin proteins with their substrate is dynamic, even for the architectural proteins that forms "stable" loops, such as CTCF and cohesin [24]. It takes energy both for chromatin proteins to interact with their substrate, as well as to preserve form.…”