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

Anat Vivante, Eugene Brozgol, Irena Bronshtein, Yuval Garini

Research output: Contribution to journalReview articlepeer-review

17 Scopus citations

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.

Original languageEnglish
Pages (from-to)128-137
Number of pages10
JournalMethods
Volume123
DOIs
StatePublished - 1 Jul 2017

Bibliographical note

Publisher Copyright:
© 2017 The Authors

Funding

This work was supported in part by Israel Centers of Research Excellence (ICORE) grant 1902/12 , Israel Science Foundation grant 51/12 and an S. Grosskopf grant for ‘Generalized dynamic measurements in live cells’.

FundersFunder number
Israel Science Foundation51/12
Israeli Centers for Research Excellence1902/12

    Keywords

    • Chromatin
    • Diffusion
    • Dynamic methods
    • Genome organization
    • Live imaging methods
    • Single Particle Tracking

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