Experimental techniques for study of chromatin mechanics in intact nuclei and living cells

Abstract

While the structure of chromatin and its physical properties have been well studied on isolated chromatin fibres and DNA strands in vitro, its organization and function in the intact interphase nucleus is less clear. Chromatin organization is critical for transcriptional regulation and DNA replication, and mounting evidence suggests that cells respond to changes in the mechanical environment with alterations in nuclear architecture that are accompanied by modifications in gene expression. Since the nucleus forms part of a continuous physical network spanning the extracellular matrix, the cytoskeleton and the nuclear envelope, environmentally mediated forces can be transmitted to the nucleus and induce deformations of the chromatin. Here, we describe a subset of techniques that can be applied to probe nuclear mechanics, ranging from micropipette aspiration to strain experiments on living cells. These experiments probe the physical properties of the nuclear envelope, the nucleoplasm, and the chromatin. We discuss the advantages and disadvantages of each technique and elaborate on their use to examine specific aspects of chromatin. In the end, a combination of these technologies can provide important insights into the delicate relationship between form and function of chromatin organization in the living cell. © 2008 Springer.