Nuclear organization and chromatin dynamics in yeast: Biophysical models or biologically driven interactions?

• Published in: Biochimica et biophysica acta Vol. 1819; no. 6; pp. 468 - 481
• Main Authors: Albert, Benjamin, Léger-Silvestre, Isabelle, Normand, Christophe, Gadal, Olivier
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2012; Elsevier
• Subjects: Biochemistry, Molecular Biology; Biophysical Phenomena; Cell Nucleus - genetics; Chromatin - genetics; Chromatin Assembly and Disassembly - genetics; Chromatin dynamics; Chromatin organization; Chromosomes - genetics; Diffusion; Gene Expression Regulation, Fungal; Genome; Life Sciences; Models, Theoretical; Nuclear pore complex; Nuclear structure; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Chromatin organization; Nuclear structure; Chromatin dynamics; Nuclear pore complex; Saccharomyces cerevisiae
• ISSN: 1874-9399; 0006-3002; 1876-4320; 1878-2434
• DOI: 10.1016/j.bbagrm.2011.12.010

Over the past decade, tremendous progress has been made in understanding the spatial organization of genes and chromosomes. Nuclear organization can be thought of as information that is not encoded in DNA, but which nevertheless impacts gene expression. Nuclear organizational influences can be cell-specific and are potentially heritable. Thus, nuclear organization fulfills all the criteria necessary for it to be considered an authentic level of epigenetic information. Chromosomal nuclear organization is primarily dictated by the biophysical properties of chromatin. Diffusion models of polymers confined in the crowded nuclear space accurately recapitulate experimental observation. Diffusion is a Brownian process, which implies that the positions of chromosomes and genes are not defined deterministically but are likely to be dictated by the laws of probability. Despite the small size of their nuclei, budding yeast have been instrumental in discovering how epigenetic information is encoded in the spatial organization of the genome. The relatively simple organization of the yeast nucleus and the very high number of genetically identical cells that can be observed under fluorescent microscopy allow statistically robust definitions of the gene and chromosome positions in the nuclear space to be constructed. In this review, we will focus on how the spatial organization of the chromatin in the yeast nucleus might impact transcription. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing. ► 3D chromatin organization in nuclear space impacts nuclear functions. ► Biophysical models of chromatin accurately recapitulate observed nuclear organization. ► Saccharomyces cerevisiae is a simple model for studying nuclear organization. ► Numerous nuclear landmarks interact with defined chromatin elements. ► Chromatin is organized by global biophysical rules and local biological interactions.