Dynamics of chromatin, proteins, and bodies within the cell nucleus Andrew Belmont A new and still evolving paradigm of a highly dynamic nucleus has emerged in recent years. This paradigm includes an inherently high turnover rate of histone and non-histone protein modifications, targeted turnover and/or displacement of ‘stable’ core histone proteins, constant flux of macromolecules through chromosomes and nuclear bodies, including transcription factors and co-activators, and an energy-dependent facilitation of nuclear-protein complex formation and disassembly. Also included are fast, local movements of chromosomes, together with slower but long-range movements of chromosomes and nuclear bodies. Addresses Department of Cell and Structural Biology, University of Illinois, Urbana-Champaign B107, Chemical and Life Science Laboratory, 601 South Goodwin Avenue, Urbana, IL 61801, USA e-mail: asbel@uiuc.edu Current Opinion in Cell Biology 2003, 15:304–310 This review comes from a themed issue on Nucleus and gene expression Edited by Jeanne Lawrence and Gordon Hager 0955-0674/03/$ – see front matter ß 2003 Elsevier Science Ltd. All rights reserved. DOI 10.1016/S0955-0674(03)00045-0 Abbreviations ChIP chromatin immunoprecipitation ER oestrogen receptor FRAP fluorescence recovery after photobleaching GFP green fluorescent protein GR glucocorticoid receptor HAT histone acetyltransferase PML promyelocytic leukaemia pol RNA polymerase SMN survival motor neuron Introduction Over the past two decades, the dynamics of the cyto- skeleton and cytoplasmic organelles have emerged as central themes in cell biology. By contrast, the interphase nucleus appeared to be the last refuge for the concept of stable cell structures and compartmentalisation. Trans- mission light microscopy of living cells revealed nuclei whose shape and internal substructures showed little apparent movement. At the molecular level, epigenetic programmes of gene activity, such as X chromosome inactivation, were demonstrated as being stable, once established, for many cell generations, even in the absence of factors required for initiation of silencing, with chromatin proteins such as histones showing little turnover. Moreover, biochemical in vitro reconstitution experiments led to sequential models of assembly for transcription pre-initiation complexes, over time periods of tens of minutes, with the idea that these complexes, once assembled, would be stable for tens of minutes to hours, as observed for transcription factor–DNA interac- tions in vitro. Here, I review recent experiments that are beginning to reveal instead a highly dynamic cell nucleus whose components are in constant flux and movement. Dynamics of chromosomal proteins DNA folding on the nucleosome surface inhibits binding of most chromosomal proteins. Slow, intrinsic nucleo- some dynamics occurs through a ‘breathing’ mechanism, most likely involving progressive uncoiling from the DNA entry or exit points on the core particle, leading to transient release of DNA from the histone surface [1  ]. Although this ‘breathing’ allows DNA binding of a wide range of proteins, the binding rate is low. ‘Pioneer’ transcription factors capable of binding to compacted nucleosome arrays and directly remodelling these arrays have been identified [2  ]. Other transcription factors that bind early in the activation process lead to chromatin remodelling through recruitment of chromatin-remodel- ling and histone-modification complexes. In both cases, chromatin remodelling and histone modifications may, through unmasking binding sites, facilitate binding of other regulatory proteins. Histone modifications can recruit other specific proteins to the site, according, to a combinatorial or ‘histone code’ [3], while in some cases changing structural properties of individual nucleosomes or their folding into higher-order chromatin structures. What is new over the past year is a growing appreciation for the existence of global histone acetylation and deacetyla- tion activity, acting over large regions of the genome in addition to locally targeted histone-modification activities [4  ]. This allows rapid reversal of targeted histone acet- ylation or deacetylation at regulatory regions after removal of the targeting signal. In yeast, using a TetR-targeted VP16 activation domain, recovery to baseline histone acetylation levels occurred within 2 min after removal of targeted histone acetyltransferases (HATs) and 6 min for targeted Rpd3 histone deacetylase [5  ]. This implies an inherently high turnover cycle of core-histone modifi- cations, in turn implying a constitutive high capacity for dynamic chromatin remodelling throughout the genome. In higher eukaryotic cells, there are indications that particular histone modifications might be targeted not 304 Current Opinion in Cell Biology 2003, 15:304–310 www.current-opinion.com